MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Bioinformation' source. Mon, 06 Feb 2012 22:09:25 +0100 http://www.medworm.com/index.php?rid=5531024&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125377%26dopt%3DAbstract Authors: Ragunath P, Chitra R, Mohammad S, Abhinand P Abstract Autism Spectrum Disorder (ASD) is a "spectrum" of disorders, characterized by varying degrees of symptoms ranging from mild to severe. Among Psychiatric disorders, Autism Spectrum Disorders have the strongest evidence for a genetic basis, yet the search for specific genes contributing to these often devastating developmental syndromes has proven extraordinarily difficult. Bipolar Disorder (BP) is a manic-depressive disorder whose symptoms are characterized by extremities in moods. It is also called as the "Mood disorder". BP, like, ASD also has a strong genetic basis and identification of the candidate genes still remains an ongoing effort. Literature studies point to the hypothesis that ASD and BP have good chances of ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531024 Fri, 23 Dec 2011 02:42:02 +0100 5531024 http://www.medworm.com/index.php?rid=5531023&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125378%26dopt%3DAbstract Authors: Unissa AN, Sudha S, Selvakumar N, Hassan S Abstract AccD6 (acetyl coenzyme A (CoA) carboxylase), plays an important role in mycolic acid synthesis of Mycobacterium tuberculosis (Mtb). Induced gene expression by isoniazid (isonicotinylhydrazine - INH), anti-tuberculosis drug) shows the expression of accD6. It is our interest to study the binding of activated INH with the AccD6 model using molecular docking procedures. The study predicts a primary binding site for activated INH (isonicotinyl acyl radical) in AccD6 as a potential target. PMID: 22125378 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531023 Fri, 23 Dec 2011 02:42:02 +0100 5531023 http://www.medworm.com/index.php?rid=5531022&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125379%26dopt%3DAbstract Authors: Gnanavel M, Serva Peddha M Abstract The prevalence of obesity and diabetes has increased exponentially in recent years around the globe, especially in India. Sweet proteins have the potential to substitute the sugars, by acting as natural, good and low calorie sweeteners. They also do not trigger a demand for insulin in diabetic patients unlike sucrose. In humans, the sweet taste perception is mainly due to taste-specific G protein-coupled heterodimeric receptors T1R2-T1R3. These receptors recognize diverse natural and synthetic sweeteners such as monelin, brazzein, thaumatin, curculin, mabinlin, miraculin and pentadin. Structural modeling of new sweetener proteins will be a great leap in further advancement of knowledge and their utility as sweeteners. We have explored th... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531022 Fri, 23 Dec 2011 02:42:02 +0100 5531022 http://www.medworm.com/index.php?rid=5531021&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125380%26dopt%3DAbstract Authors: Zubaer A, Thapa S Abstract Different subtypes of Influenza A virus are associated with species specific, zoonotic or pandemic Influenza. The cause of its severity underlies in complicated evolution of its segmented RNA genome. Although genetic shift and genetic drift are well known in the evolution of this virus, we reported the significant role of unique RNA palindromes in its evolution. Our computational approach identified the existence of unique palindromes in each subtype of Influenza A virus with its absence in Influenza B relating the fact of virulence and vigorous genetic hitchhiking in Influenza A. The current study focused on the re-assortment event responsible for the emergence of pandemic-2009 H1N1 virus, which is associated with outgrow of new palindrome and i... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531021 Fri, 23 Dec 2011 02:42:02 +0100 5531021 http://www.medworm.com/index.php?rid=5531020&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125381%26dopt%3DAbstract Authors: Yang X, Yan Y Abstract The histone octamer induced bending of DNA into the super-helix structure in nucleosome core particle, is very unique and vital for DNA packing into chromatin. We collected 48 nucleosome crystal structures from PDB and applied a multivariate analysis on the nucleosome structural data. Based on the anisotropic nature of DNA structure, a principal conformational subspace (PCS) is derived from multiple properties to represent the most significant variances of nucleosome DNA structures. The coupling of base pair-oriented parameters with sugar phosphate backbone parameters presented in principal dimensionalities reveals two main deformation modes that have supplemented the existing physical model. By using sequence alignment-based statistics, a positionde... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531020 Fri, 23 Dec 2011 02:42:02 +0100 5531020 http://www.medworm.com/index.php?rid=5531019&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125382%26dopt%3DAbstract Authors: Khedidja B, Abderrahman L Abstract Infections caused by Candida species manifest in a number of diseases, including candidemia, vulvovaginal candidiasis, endocarditis, and peritonitis. Candida species have been reported to possess lipolytic activity due to the secretion of lipolytic enzymes such as esterases, lipases and phospholipases. Extra-cellular hydrolytic enzymes seem to play an important role in Candida overgrowth. Candidiasis is commonly treated with antimycotics such as clotrimazole and nystatin. The antimycotics bind to a major component of the fungal cell membrane (ergosterol), forming pores that lead to death of the fungus. However, the secondary effects caused during such treatment have aroused a need to develop a treatment based on lipase inhibition. Nonethe... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531019 Fri, 23 Dec 2011 02:42:02 +0100 5531019 http://www.medworm.com/index.php?rid=5531018&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125383%26dopt%3DAbstract Authors: Sundaramurthi JC, Kumar S, Silambuchelvi K, Hanna LE Abstract The Mycobacterium tuberculosis genome codes for 20 different cytochromes. These cytochromes are involved in the breakdown of recalcitrant pollutants and the synthesis of polyketide antibiotics and other complex macromolecules. It has been demonstrated that CYP121 is essential for viability of the bacterium by gene knock-out and complementation studies. CYP121 could therefore be a probable target for the development of new drugs for TB. It has been widely reported that orthologs of CYP121 in fungi are inhibited by azole drugs. We evaluated whether these azole drugs or their structural analogs could bind to and inhibit CYP121 of M. tuberculosis using molecular docking. Six molecules with known anti-CYP121 activity... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531018 Fri, 23 Dec 2011 02:42:02 +0100 5531018 http://www.medworm.com/index.php?rid=5531017&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125384%26dopt%3DAbstract Authors: Vijayakumar B, Umamaheswari A, Puratchikody A, Velmurugan D Abstract Histone deacetylases (HDACs) are enzymes, which catalyze the removal of acetyl moiety from acetyl-lysine within the histone proteins and promote gene repression and silencing resulting in several types of cancer. HDACs are important therapeutic targets for the treatment of cancer and related diseases. Hydroxamic acid inhibitors show promising results in clinical trials against carcinogenesis. 120 hydroxamic acid derivatives were designed as inhibitors based on hydrophobic pocket and the Zn (II) catalytic site of HDAC8 active site using Structure Based Drug Design (SBDD) approach. High Throughput Virtual screening (HTVs) was used to filter the effective inhibitors. Induced Fit Docking (IFD) studies were ca... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531017 Fri, 23 Dec 2011 02:42:02 +0100 5531017 http://www.medworm.com/index.php?rid=5531016&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125385%26dopt%3DAbstract Authors: Moorthy K, Mohamad MS Abstract A random forest method has been selected to perform both gene selection and classification of the microarray data. In this embedded method, the selection of smallest possible sets of genes with lowest error rates is the key factor in achieving highest classification accuracy. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. The option for biggest subset selection is done to assist researchers who intend to use the informative genes for further research. Enhanced random forest gene selection has performed better in terms of selecting the smallest subset as well as biggest subset of informative genes with lowest out of b... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531016 Fri, 23 Dec 2011 02:42:02 +0100 5531016 http://www.medworm.com/index.php?rid=5531015&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125386%26dopt%3DAbstract Authors: Salahuddin P, Khan AU Abstract Influenza A virus subtype H5N1, also known as "bird flu" has been documented to cause an outbreak of respiratory diseases in humans. The unprecedented spread of highly pathogenic avian influenza type A is a threat to veterinary and human health. The BFluenza is a relational database which is solely devoted to proteomic information of H5N1 subtype. Bfluenza has novel features including computed physico-chemical properties data of H5N1 viral proteins, modeled structures of viral proteins, data of protein coordinates, experimental details, molecular description and bibliographic reference. The database also contains nucleotide and their decoded protein sequences data. The database can be searched in various modes by setting search options. The s... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531015 Fri, 23 Dec 2011 02:42:02 +0100 5531015 http://www.medworm.com/index.php?rid=5531014&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125387%26dopt%3DAbstract Authors: Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ Abstract The Comparative Toxicogenomics Database (CTD) is a free resource that describes chemical-gene-disease networks to help understand the effects of environmental exposures on human health. The database contains more than 13,500 chemical-disease and 14,200 gene-disease interactions. In CTD, chemicals and genes are associated with a disease via two types of relationships: as a biomarker or molecular mechanism for the disease (M-type) or as a real or putative therapy for the disease (T-type). We leveraged these curated datasets to compute similarity indices that can be used to produce lists of comparable diseases ("DiseaseComps") based upon shared toxicogenomic profiles. This new metric now classifies diseases with commo... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531014 Fri, 23 Dec 2011 02:42:02 +0100 5531014 http://www.medworm.com/index.php?rid=5531013&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125388%26dopt%3DAbstract Authors: Horiike T, Miyata D, Tateno Y, Minai R Abstract Horizontal gene transfer (HGT) is a common event in prokaryotic evolution. Therefore, it is very important to consider HGT in the study of molecular evolution of prokaryotes. This is true also for conducting computer simulations of their molecular phylogeny because HGT is known to be a serious disturbing factor for estimating their correct phylogeny. To the best of our knowledge, no existing computer program has generated a phylogenetic tree with HGT from an original phylogenetic tree. We developed a program called HGT-Gen that generates a phylogenetic tree with HGT on the basis of an original phylogenetic tree of a protein or gene. HGT-Gen converts an operational taxonomic unit or a clade from one place to another in a given... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531013 Fri, 23 Dec 2011 02:42:02 +0100 5531013 http://www.medworm.com/index.php?rid=5531012&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125389%26dopt%3DAbstract Authors: Nagarathnam B, Sankar K, Dharnidharka V, Balakrishnan V, Archunan G, Sowdhamini R Abstract Multiple sequence alignments become biologically meaningful only if conserved and functionally important residues and secondary structural elements preserved can be identified at equivalent positions. This is particularly important for transmembrane proteins like G-protein coupled receptors (GPCRs) with seven transmembrane helices. TM-MOTIF is a software package and an effective alignment viewer to identify and display conserved motifs and amino acid substitutions (AAS) at each position of the aligned set of homologous sequences of GPCRs. The key feature of the package is to display the predicted membrane topology for seven transmembrane helices in seven colours (VIBGYOR colouring sc... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531012 Fri, 23 Dec 2011 02:42:02 +0100 5531012 http://www.medworm.com/index.php?rid=5531011&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125390%26dopt%3DAbstract This study mainly evaluates the potential use of botanicals against MRSA infections. Computer aided design is an initial platform to screen novel inhibitors and the data finds applications in drug development. The drug-likeness and efficiency of various herbal compounds were screened by ADMET and docking studies. The virulent factor of most of the MRSA associated infections are Penicillin Binding Protein 2A (PBP2A) and Panton-Valentine Leukocidin (PVL). Hence, native structures of these proteins (PDB: 1VQQ and 1T5R) were used as the drug targets. The docking studies revealed that the active component of Aloe vera, β-sitosterol (3S, 8S, 9S, 10R, 13R, 14S, 17R) -17- [(2R, 5R)-5-ethyl-6-methylheptan-2-yl] -10, 13-dimethyl 2, 3, 4, 7, 8, 9, 11, 12, 14, 15, 16, 17- dodecahydro-1H-cyclopenta [a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531011 Fri, 23 Dec 2011 02:42:02 +0100 5531011 http://www.medworm.com/index.php?rid=5531010&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125391%26dopt%3DAbstract Authors: Karunakar P, Krishnamurthy V, Girija CR, Krishna V, Vasundhara DE, Begum NS, Syed AA Abstract The structure of α-Cyano-3-phenoxybenzyl-2-(4-chlorophenyl)-3-methylbutyrate (Fenvalarate) has been established by X-ray crystallography to understand the structure-activity relationship, which is of paramount importance in the toxicological studies of the compound. Fenvalarate is stabilized by intermolecular C-H…O, C-H…Cl, C-H…π and C-H…N interactions which are responsible for the stability of the compound and its interaction with the Actin. The crystallographic coordinates of the compound was extrapolated to docking studies to elucidate the action of fenvalarate against neural cytoskeletal protein of insect and mammalian β-actin. A strong affinity was observed in bind... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531010 Fri, 23 Dec 2011 02:42:02 +0100 5531010 http://www.medworm.com/index.php?rid=5531009&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125392%26dopt%3DAbstract Authors: Laskar A, Rodger EJ, Chatterjee A, Mandal C Abstract Serine proteases are an abundant class of enzymes that are involved in a wide range of physiological processes and are classified into clans sharing structural homology. The active site of the subtilisin-like clan contains a catalytic triad in the order Asp, His, Ser (S8 family) or a catalytic tetrad in the order Glu, Asp and Ser (S53 family). The core structure and active site geometry of these proteases is of interest for many applications. The aim of this study was to investigate the structural properties of different S8 family serine proteases from a diverse range of taxa using molecular modeling techniques. In conjunction with 12 experimentally determined three-dimensional structures of S8 family members, our predic... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531009 Fri, 23 Dec 2011 02:42:02 +0100 5531009 http://www.medworm.com/index.php?rid=5531008&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125393%26dopt%3DAbstract We report the screening of various 2,3-disubstituted-4(3H)-quinazolinones possessing benzenesulfonamide moiety, directly or indirectly bound to the ring system, using the Protein-Ligand ANT System (PLANTS) docking software against the COX-2 enzyme. Various molecular structures of ligands were docked and scored to identify structurally similar ligands to SC-558 (reference ligand) in binding interaction to COX-2 binding site. The results show that 2,3-disubstituted-4(3H)-quinazolinones possess pbenzenesulfonamide moiety at C-2, and phenyl moiety at N-3 binds directly or indirectly to the ring system with high binding affinity. The docked ligand has orientations similar to that observed with SC-558 satisfying Lipinski's rule of five. PMID: 22125393 [PubMed - in process] (Source: Bioinform... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531008 Fri, 23 Dec 2011 02:42:02 +0100 5531008 http://www.medworm.com/index.php?rid=5531007&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125394%26dopt%3DAbstract Authors: Yi G, Jung J Abstract Identifying genomic regions that descended from a common ancestor helps us study the gene function and genome evolution. In distantly related genomes, clusters of homologous gene pairs are evidently used in function prediction, operon detection, etc. Currently, there are many kinds of computational methods that have been proposed defining gene clusters to identify gene families and operons. However, most of those algorithms are only available on a data set of small size. We developed an efficient gene clustering algorithm that can be applied on hundreds of genomes at the same time. This approach allows for large-scale study of evolutionary relationships of gene clusters and study of operon formation and destruction. An analysis of proposed algorithms ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531007 Fri, 23 Dec 2011 02:42:02 +0100 5531007 http://www.medworm.com/index.php?rid=5531006&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125395%26dopt%3DAbstract Authors: Jiang H, Ching WK Abstract Human longevity is a complex phenotype that has a significant genetic predisposition. Like other biological processes, ageing process is governed through the regulation of signaling pathways and transcription factors. The DNA damage theory of ageing suggests that ageing is a consequence of un-repaired DNA damage accumulation. Intensive research has been carried out to elucidate the role of DNA repair systems in the ageing process. Decision Trees and Naive Bayesian Algorithm are two data-mining based classification methods for systematically analyzing data about human DNA repair genes. In this paper we develop a linearly combined kernel with Support Vector Machine (SVM) to analyze the ageing related data. The popular supervised learning algorithm ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531006 Fri, 23 Dec 2011 02:42:02 +0100 5531006 http://www.medworm.com/index.php?rid=5531005&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125396%26dopt%3DAbstract This study concentrates on comparative analysis of genic microsatellites in nine important legume (Arachis hypogaea, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus, Medicago truncatula, Phaseolus vulgaris, Pisum sativum and Vigna unguiculata) and two model plant species (Oryza sativa and Arabidopsis thaliana). Screening of a total of 228090 putative unique sequences spanning 219610522 bp using a microsatellite search tool, MISA, identified 12.18% of the unigenes containing 36248 microsatellite motifs excluding mononucleotide repeats. Frequency of legume unigene-derived SSRs was one SSR in every 6.0 kb of analyzed sequences. The trinucleotide repeats were predominant in all the unigenes with the exception of C. cajan, which showed prevalence of dinucleotide repeats over trinuc... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531005 Fri, 23 Dec 2011 02:42:02 +0100 5531005 http://www.medworm.com/index.php?rid=5531004&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125397%26dopt%3DAbstract Authors: Oluwadara O, Barkhordarian A, Giacomelli L, Brant X, Chiappelli F Abstract In the U.S., nasopharyngeal carcinoma (NpC) kills >7,600 each year. Deaths are predominantly among adult men, and in most cases, early detection and treatment can save lives. Despite the annual spending of approximately 3.2 billion dollars on head and neck cancer research, NpC remains a neglected disease since its fatality rates are among the lowest nation wide. The relative survival rates from NpC have not improved in the U.S. in the last 20 years. Infection with Epstein Barr Virus (EBV) is an important co-factor in the etiology of NpC. In other regions of the word (e.g., South-East Asia, Latin America), EBV infection and NpCrelated prevalence and mortality are substantially higher and more alar... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5531004 Fri, 23 Dec 2011 02:42:02 +0100 5531004 http://www.medworm.com/index.php?rid=5438660&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102770%26dopt%3DAbstract Authors: Cong TV, Groeneveld E Abstract Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information sy... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438660 Wed, 23 Nov 2011 23:00:03 +0100 5438660 http://www.medworm.com/index.php?rid=5438659&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102771%26dopt%3DAbstract Authors: Hussein ZA, Loke KK, Abidin RA, Othman R Abstract Functional genomics has proven to be an efficient tool in identifying genes involved in various biological functions. However the availability of commercially important seaweed Eucheuma denticulatum functional resources is still limited. EuDBase is the first seaweed online repository that provides integrated access to ESTs of Eucheuma denticulatum generated from samples collected from Kudat and Semporna in Sabah, Malaysia. The database stored 10,031 ESTs that are clustered and assembled into 2,275 unique transcripts (UT) and 955 singletons. Raw data were automatically processed using ESTFrontier, an in-house automated EST analysis pipeline. Data was collected in MySQL database. Web interface is implemented using PHP and it ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438659 Wed, 23 Nov 2011 23:00:03 +0100 5438659 http://www.medworm.com/index.php?rid=5438658&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102772%26dopt%3DAbstract We describe the prediction of protein "hub" using physiochemical, thermodynamic and conformational properties of amino acid residues in sequence. We have used twenty sequence based features to identify hub behaviour. Linear discriminant analysis and normalised Bayesian approach were utilized for identifying hub proteins solely using these sequence features in E. coli/H. sapiens datasets with accuracies of 99.5/98.6, 87.8/89.6 and 90.1/92.6, respectively. PMID: 22102772 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438658 Wed, 23 Nov 2011 23:00:03 +0100 5438658 http://www.medworm.com/index.php?rid=5438657&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102773%26dopt%3DAbstract Authors: Misman MF, Mohamad MS, Deris S, Abdullah A, Hashim SZ Abstract Pathway analysis has lead to a new era in genomic research by providing further biological process information compared to traditional single gene analysis. Beside the advantage, pathway analysis provides some challenges to the researchers, one of which is the quality of pathway data itself. The pathway data usually defined from biological context free, when it comes to a specific biological context (e.g. lung cancer disease), typically only several genes within pathways are responsible for the corresponding cellular process. It also can be that some pathways may be included with uninformative genes or perhaps informative genes were excluded. Moreover, many algorithms in pathway analysis neglect these limitatio... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438657 Wed, 23 Nov 2011 23:00:03 +0100 5438657 http://www.medworm.com/index.php?rid=5438656&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102774%26dopt%3DAbstract Authors: Das R, Shimamoto T, Hosen SM, Arifuzzaman M Abstract The multi-copy single-stranded DNA (msDNA) is yielded by the action of reverse transcriptase of retro-element in a wide range of pathogenic bacteria. Upon this phenomenon, it has been shown that msDNA is only produced by Eubacteria because many Eubacteria species contained reverse transcriptase in their special retro-element. We have screened around 111 Archaea at KEGG (Kyoto Encyclopedia of Genes and Genomes) database available at genome net server and observed three Methanosarcina species (M.acetivorans, M.barkeri and M.mazei), which also contained reverse transcriptase in their genome sequences. This observation of reverse transcriptase in Archaea raises questions regarding the origin of this enzyme. The evolutionary ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438656 Wed, 23 Nov 2011 23:00:03 +0100 5438656 http://www.medworm.com/index.php?rid=5438655&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102775%26dopt%3DAbstract We describe the analysis of MAPK EST sequences from Curcuma longa (an asexually reproducible plant of great medicinal and economic significance). The four Curcuma MAPKs contains all 11 MAPK conserved domains and phosphorylation-activation motif, TEY. Phylogenetic analysis grouped them in the subgroup A and C as identified earlier for Arabidopsis. The Curcuma MAPKs identified showed high sequence homology to rice OsMPK3, OsMPK4 and OsMPK5 suggesting the presence of similar key element in signaling biotic and abiotic stress responses. Although further in vivo and in vitro analysis are required to establish the physiological role of Curcuma MAPKs, this study provides the base for future research on diverse signaling pathways mediated by MAPKs in Curcuma longa as well as other asexually reprod... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438655 Wed, 23 Nov 2011 23:00:03 +0100 5438655 http://www.medworm.com/index.php?rid=5438654&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102776%26dopt%3DAbstract Authors: Oezguen N, K Mantha A, Izumi T, H Schein C, Mitra S, Braun W Abstract Apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the base excision repair pathway, cleaves damaged DNA in Mg(2+) dependent reaction. Despite characterization of nine X-ray crystallographic structures of human APE1, in some cases, bound to various metal ions and substrate/product, the position of the metal ion and its stoichiometry for the cleavage reaction are still being debated. While a mutation of the active site E96Q was proposed to eliminate Mg(2+) binding at the "A" site, we show experimentally that this mutant still requires Mg(2+) at concentration similar to that for the wild type enzyme to cleave the AP site in DNA. Molecular dynamics simulations of the wild type APE1, E96Q and a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438654 Wed, 23 Nov 2011 23:00:03 +0100 5438654 http://www.medworm.com/index.php?rid=5438653&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102777%26dopt%3DAbstract Authors: Vinuchakkaravarthy T, Kumaravel KP, Ravichandran S, Velmurugan D Abstract Novel compounds with significant medicinal properties have gained much interest in therapeutic approaches for treating various inflammatory disorders like arthritis, odema and snake bites and the post-envenom (impregnating with venom) consequences. Inflammation is caused by the increased concentration of secretory Phospholipases A(2) (sPLA(2)s) at the site of envenom. A novel compound Tris(2,4-di-tert-butylphenyl) phosphate (TDTBPP) was isolated from the leaves of Vitex negundo and the crystal structure was reported recently. The acute anti-inflammatory activity of TDTBPP was assessed by Carrageenan-induced rat paw odema method. TDTBPP reduced the raw paw odema volume significantly at the tested dose... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438653 Wed, 23 Nov 2011 23:00:03 +0100 5438653 http://www.medworm.com/index.php?rid=5438652&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22102778%26dopt%3DAbstract In this study, a three-dimensional model of human P450 4F22 was constructed by comparative modeling using Modeller 9v5. The resulting model was refined by energy minimization subjected to the quality assessment from both geometric and energetic aspects and was found to be of reasonable quality. Docking approach was employed to dock arachidonic acid into the active site of CYP4F22 in order to probe the ligand-binding modes. As a result, several key residues were identified to be responsible for the binding of arachidonic acid with CYP4F22. These findings provide useful information for understanding the biological roles of CYP4F22 and structure-based drug design. PMID: 22102778 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5438652 Wed, 23 Nov 2011 23:00:03 +0100 5438652 http://www.medworm.com/index.php?rid=5295202&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21976864%26dopt%3DAbstract Authors: Baba N, Akaho E Abstract Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platform. This is a user-friendly, flexible, and versatile tool which can be used by users who are familiar with Windows OS. The virtual screening performance was tested for an arbitrarily-selected receptor, FGFR tyrosine kinase (pdb code: 1agw), by using ligands downloaded from ZINC database with its grid size of x,y,z = 30,30,30 and run number of 10. It took 90 minutes for 100 molecules for this virtual screening. VSDK is freely available at the designated ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5295202 Sat, 08 Oct 2011 14:49:46 +0100 5295202 http://www.medworm.com/index.php?rid=5275639&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938204%26dopt%3DAbstract Authors: Mishra V, Siva Prasad CV Abstract Ricin is known as a potent toxin against animals. It consists of two chains, Ricin Toxin A (RTA) and Ricin Toxin B (RTB). The toxic effect is known to be caused by RTA. Inhibitors for RTA with less efficiency have been reported. Hence, it is of interest to identify new inhibitors. Virtual screening methods (computer aided drug designing) to find similar molecules in drug database were used for screening new inhibitors against RTA. We used the structure of RTA in complex with Pteroic acid (PDB code: 1BR6) as target molecule. Ligand based virtual screening approach was used in which the known inhibitory molecule Pteroic acid (PTA) served as a template to identify similar ligands from the ZINC database. These ligands were docked inside the bi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275639 Mon, 03 Oct 2011 12:50:02 +0100 5275639 http://www.medworm.com/index.php?rid=5275638&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938205%26dopt%3DAbstract Authors: Elgamacy MA, Shalaby RA, Elkodsh AT, Kamel AF, Elsayed MS, Abou-El-Ella DA Abstract We are reporting the discovery of small molecule inhibitors for vascular endothelial growth factor receptor type 2 (VEGFR-2) extracellular domain. The VEGFR-2 extracellular domain is responsible for the homo-dimerization process, which has been recently reported as a main step in VEGFR signal transduction cascade. This cascade is essential for the vascularization and survival of most types of cancers. Two main design strategies were used; Molecular docking-based Virtual Screening and Fragment Based Design (FBD). A virtual library of drug like compounds was screened using a cascade of docking techniques in order to discover an inhibitor that binds to this new binding site. Rapid docking meth... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275638 Mon, 03 Oct 2011 12:50:02 +0100 5275638 http://www.medworm.com/index.php?rid=5275637&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938206%26dopt%3DAbstract Authors: Salman M, Malleda C, Suneel NA, Qureshi IA, Frank EA, D'Souza CJ Abstract Human serum paraoxonase1 (HuPON1) belongs to the family of A-esterases (EC.3.1.8.1). It is associated with HDL particle and prevents atherosclerosis by cleaving lipid hydroperoxides and other proatherogenic molecules of oxidized low density lipoproteins (LDL). Since the precise structure of HuPON1 is not yet available, the structure-function relationship between HuPON1 and activators/inhibitors is still unknown. Therefore, a theoretical model of HuPON1 was generated using homology modelling and precise molecular interactions of an activator aspirin and an inhibitor cefazolin with PON1 were studied using Autodock software. The ligand binding residues were found to be similar to the predicted active si... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275637 Mon, 03 Oct 2011 12:50:02 +0100 5275637 http://www.medworm.com/index.php?rid=5275636&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938207%26dopt%3DAbstract Authors: Tian D, Wang Y, Zheng T Abstract In early 2009, new swine-origin influenza A (H1N1) virus emerged in Mexico and the United States. The emerging influenza virus had made global influenza pandemic for nearly one year. To every emerging pathogen, exploring the origin sources is vital for viral control and clearance. Influenza virus is different from other virus in that it has 8 segments, making the segment reassortment a main drive in virus evolution. In exploring reassortment evolution origins of a newly emerging influenza virus, integrated comparing of the origin sources of all the segments is necessary. If some segments have high homologous with one parental strain, lower homologous with another parental strain, while other segments are reverse, can we proposed that this e... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275636 Mon, 03 Oct 2011 12:50:02 +0100 5275636 http://www.medworm.com/index.php?rid=5275635&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938208%26dopt%3DAbstract Authors: Tomar AK, Sooch BS, Yadav S Abstract Glycoproteins have immense clinical importance and comparative glycoproteomics has become a powerful tool for biomarker discovery and disease diagnosis. Seminal plasma glycoproteins participate in fertility related processes including sperm-egg recognition, modulation of capacitation and acrosome reaction inhibition. Affinity chromatography using broad specificity lectin such as Con A is widely applied for glycoproteins enrichment. More notably, Con A-interacting fraction of human seminal plasma has decapacitating activity which makes this fraction critically important. In our previous study, we isolated Con A-interacting glycoproteins from human seminal plasma and subsequently identified them by mass spectrometry. Here, we report the c... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275635 Mon, 03 Oct 2011 12:50:02 +0100 5275635 http://www.medworm.com/index.php?rid=5275634&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938209%26dopt%3DAbstract Authors: Shil P, Chavan SS, Cherian SS Abstract Antigenic drift and shift involving the surface proteins of Influenza virus gave rise to new strains that caused epidemics affecting millions of people worldwide over the last hundred years. Variations in the membrane proteins like Hemagglutinin (HA) and Neuraminidase (NA) necessitates new vaccine strains to be updated frequently and poses challenge to effective vaccine design. Though the HA protein, the primary target of the human immune system, has been well studied, reports on the antigenic variability in the other membrane protein NA are sparse. In this paper we investigate the molecular basis of antigenic drift in the NA protein of the Influenza A/H3N2 vaccine strains between 1968 and 2009 and proceed to establish correlation bet... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275634 Mon, 03 Oct 2011 12:50:02 +0100 5275634 http://www.medworm.com/index.php?rid=5275633&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938210%26dopt%3DAbstract Authors: Dwivedi N, Mishra BN, Katoch VM Abstract A quantitative structure activity relationship study was performed on different groups of anti-tuberculosis drug compound for establishing quantitative relationship between biological activity and their physicochemical /structural properties. In recent years, a large number of herbal drugs are promoted in treatment of tuberculosis especially due to the emergence of MDR (multi drug resistance) and XDR (extensive drug resistance) tuberculosis. Multidrug-resistant TB (MDR-TB) is resistant to front-line drugs (isoniazid and rifampicin, the most powerful anti-TB drugs) and extensively drug-resistant TB (XDR-TB) is resistant to front-line and second-line drugs. The possibility of drug resistance TB increases when patient does not take pre... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275633 Mon, 03 Oct 2011 12:50:02 +0100 5275633 http://www.medworm.com/index.php?rid=5275632&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938211%26dopt%3DAbstract Authors: Alexiou AT, Psiha MM, Vlamos PM Abstract A permutation-based algorithm is introduced for the representation of closed RNA secondary structures. It is an efficient 'loopless' algorithm, which generates the permutations on base-pairs of 'k-noncrossing' setting partitions. The proposed algorithm reduces the computational complexity of known similar techniques in O(n), using minimal change ordering and transposing of not adjacent elements. PMID: 21938211 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275632 Mon, 03 Oct 2011 12:50:02 +0100 5275632 http://www.medworm.com/index.php?rid=5275631&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938212%26dopt%3DAbstract Authors: Chaturvedi A, Tiwari S, Jesudasan RA Abstract The non-coding fraction of the human genome, which is approximately 98%, is mainly constituted by repeats. Transpositions, expansions and deletions of these repeat elements contribute to a number of diseases. None of the available databases consolidates information on both tandem and interspersed repeats with the flexibility of FASTA based homology search with reference to disease genes. Repeats in diseases database (RiDs db) is a web accessible relational database, which aids analysis of repeats associated with Mendelian disorders. It is a repository of disease genes, which can be searched by FASTA program or by limitedor free- text keywords. Unlike other databases, RiDs db contains the sequences of these genes with access to ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275631 Mon, 03 Oct 2011 12:50:02 +0100 5275631 http://www.medworm.com/index.php?rid=5275630&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938213%26dopt%3DAbstract We describe a database called 'Database of Drug Targets for Resistant Pathogens' (DDTRP). The database contains information on drugs with reported resistance, their respective targets, metabolic pathways involving these targets, and a list of potential alternate targets for seven pathogens. The database can be accessed freely at http://bmi.icmr.org.in/DDTRP. PMID: 21938213 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5275630 Mon, 03 Oct 2011 12:50:02 +0100 5275630 http://www.medworm.com/index.php?rid=5244907&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21927545%26dopt%3DAbstract Authors: Mishra P, Pandey PN Abstract The number of amino acid sequences is increasing very rapidly in the protein databases like Swiss-Prot, Uniprot, PIR and others, but the structure of only some amino acid sequences are found in the Protein Data Bank. Thus, an important problem in genomics is automatically clustering homologous protein sequences when only sequence information is available. Here, we use graph theoretic techniques for clustering amino acid sequences. A similarity graph is defined and clusters in that graph correspond to connected subgraphs. Cluster analysis seeks grouping of amino acid sequences into subsets based on distance or similarity score between pairs of sequences. Our goal is to find disjoint subsets, called clusters, such that two criteria are satisfied:... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5244907 Fri, 23 Sep 2011 04:52:02 +0100 5244907 http://www.medworm.com/index.php?rid=5217446&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904422%26dopt%3DAbstract Authors: Kumar S, Carugo O Abstract Filamins are dimeric actin-binding proteins participating in the organization of the actin-based cytoskeleton. Their modular domain organization is made up of an N-terminal actin-binding domain composed of two CH domains followed by flexible rod regions that consist of 24 Ig-like domains. Homology modeling was used to model human filamin using Modeller 9v5. The resulting model assessed by Verify 3D and PROCHECK showed that the final model is reliable. The conformational disorder prediction of human filamin residues were also mapped on the validated structure of human filamin. Prediction of protein disorder in filamin structures will help structural biologists to find suitable targets to be analyzed and for understanding protein function. PMID... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217446 Wed, 14 Sep 2011 08:48:02 +0100 5217446 http://www.medworm.com/index.php?rid=5217445&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904423%26dopt%3DAbstract Authors: Magray MS, Kumar A, Rawat AK, Srivastava S Abstract A bacterial strain, designated BzDS03 was isolated from water sample, collected from Dal Lake Srinagar. The strain was characterized by using 16S ribosomal RNA gene and 16S-23S rRNA internal transcribed spacer region sequences. Phylogenetic analysis showed that 16S rRNA sequence of the isolate formed a monophyletic clade with genera Escherichia. The closest phylogenetic relative was Escherichia coli with 99% 16S rRNA gene sequence similarity. The result of Ribosomal database project's classifier tool revealed that the strain BzDS03 belongs to genera Escherichia.16S rRNA sequence of isolate was deposited in GenBank with accession number FJ961336. Further analysis of 16S-23S rRNA sequence of isolate confirms that the identi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217445 Wed, 14 Sep 2011 08:48:02 +0100 5217445 http://www.medworm.com/index.php?rid=5217444&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904424%26dopt%3DAbstract Authors: Skariyachan S, Mahajanakatti AB, Sharma N, Sevanan M Abstract Clostridium perfringens (a versatile pathogenic bacterium) secretes enterotoxins (the deltatoxin, virulent factor) and causes food borne gastroenteritis and gasgangrene. The organism was isolated and characterized from improperly cooked meat and poultry samples. The isolated organism showed multiple drug resistance indicating that the treatment is challenging. Hence, there is need for improved therapeutic agents. The rational design of improved therapeutics requires the crystal structure for the toxin. However, the structure for the toxin is not yet available in its native form. Thus, we modeled the toxin structure using α- hemolysin of Staphylococcus aureus (PDB: 3M4D chain A) as template. The docking of the t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217444 Wed, 14 Sep 2011 08:48:02 +0100 5217444 http://www.medworm.com/index.php?rid=5217443&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904425%26dopt%3DAbstract In this study, a support vector machine (SVM)- based method, SSPred was developed for the automated functional annotation of proteins involved in secretion systems further classifying them into five major sub-types (Type-I, Type-II, Type-III, Type-IV and Sec systems). The dataset used in this study for training and testing was obtained from KEGG and SwissProt database and was curated in order to avoid redundancy. To overcome the problem of imbalance in positive and negative dataset, an ensemble of SVM modules, each trained on a balanced subset of the training data were used. Firstly, protein sequence features like amino-acid composition (AAC), dipeptide composition (DPC) and physico-chemical composition (PCC) were used to develop the SVM-based modules that achieved an average accuracy of 8... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217443 Wed, 14 Sep 2011 08:48:02 +0100 5217443 http://www.medworm.com/index.php?rid=5217442&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904426%26dopt%3DAbstract We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily. PMID: 21904426 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217442 Wed, 14 Sep 2011 08:48:02 +0100 5217442 http://www.medworm.com/index.php?rid=5217441&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904427%26dopt%3DAbstract Authors: Li F, Seillier-Moiseiwitsch F Abstract Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface for differential analysis of 2D gel images. The user-friendly software, RegStatGel, contains fully automated as well as interactive procedures. It was developed and has been tested under Matlab 7.01. AVAILABILITY: The database is available for free at http://www.mediafire.com/FengLi/2DGelsoftware. PMID: 21904427 [PubMed - in process] (Source: Bioinform... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217441 Wed, 14 Sep 2011 08:48:02 +0100 5217441 http://www.medworm.com/index.php?rid=5217440&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904428%26dopt%3DAbstract Authors: Jayakodi M, Selvan SG, Natesan S, Muthurajan R, Duraisamy R, Ramineni JJ, Rathinasamy SA, Karuppusamy N, Lakshmanan P, Chokkappan M Abstract The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE - CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly av... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217440 Wed, 14 Sep 2011 08:48:02 +0100 5217440 http://www.medworm.com/index.php?rid=5217439&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904429%26dopt%3DAbstract Authors: Joseph J, Rajendran V, Hassan S, Kumar V Abstract Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217439 Wed, 14 Sep 2011 08:48:02 +0100 5217439 http://www.medworm.com/index.php?rid=5217438&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904430%26dopt%3DAbstract We describe the docking of 26 withanferin and 14 withanolides from Withania somnifera into the three dimensional structure of PknG of M. tuberculosis using GLIDE. The inhibitor binding positions and affinity were evaluated using scoring functions- Glidescore. The withanolide E, F and D and Withaferin - diacetate 2 phenoxy ethyl carbonate were identified as potential inhibitors of PknG. The available drug molecules and the ligand AX20017 showed hydrogen bond interaction with the aminoacid residues Glu233 and Val235. In addition to Val235 the other amino acids, Gly237, Gln238 and Ser239 are important for withanolide inhibitor recognition via hydrogen bonding mechanisms. PMID: 21904430 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217438 Wed, 14 Sep 2011 08:48:02 +0100 5217438 http://www.medworm.com/index.php?rid=5217437&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904431%26dopt%3DAbstract Authors: Banerjee K, Gupta U, Gupta S, Sharma SK, Jain CK Abstract Invasive fungal opportunistic infections or mycoses have been on the rise with increase in the number of immuno-compromised patients accounting for associated high morbidity and mortality rates. The antifungal drugs are not completely effective due to increased resistance and varied susceptibility of fungi. Hence, the functional diversification study of novel targets has to be carried out. The enzyme glucosamine-6-phosphate synthase [EC 2.6.1.16], a novel drug target, catalyzes the rate-limiting step of the fungal cell-wall biosynthetic pathway, comprising four conserved domains, two glutaminase and sugar-isomerising (SIS) domains with active site. The amino acids within these domains tend to mutate simultaneously a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217437 Wed, 14 Sep 2011 08:48:02 +0100 5217437 http://www.medworm.com/index.php?rid=5217436&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904432%26dopt%3DAbstract In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Hepatitis B virus (HBV). Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by HBV. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. We find that some nodes in the network that prove to be topologically important, in particular HBx is also known to be important target protein used for the treatment of HBV. Therefore, HBx protein is the preferential choice for inhibition to stop the proteolytic processing. Hence, the 3D structu... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217436 Wed, 14 Sep 2011 08:48:02 +0100 5217436 http://www.medworm.com/index.php?rid=5217435&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904433%26dopt%3DAbstract Authors: Nagarathnam B, Kannan S, Dharnidharka V, Balakrishnan V, Archunan G, Sowdhamini R Abstract G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. GPCRs retain a characteristic membrane topology of seven alpha helices with three intracellular, three extracellular loops and flanking N' and C' terminal residues. Subtle differences do exist in the helix boundaries (TM-domain), loop lengths, sequence features such as conserved motifs, and substituting amino acid patterns and their physiochemical properties amongst these sequences (clusters) at intra-genomic and inter-genomic level (please re-phrase into 2 statements for clarity). In the current study, we employ prediction of helix boundaries a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217435 Wed, 14 Sep 2011 08:48:02 +0100 5217435 http://www.medworm.com/index.php?rid=5217434&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904434%26dopt%3DAbstract Authors: Dinesh , Goswami A, Suresh PS, Thirunavukkarasu C, Weiergräber OH, Kumar MS Abstract The neutral sphingomyelinase (N-SMase) is considered a major candidate for mediating the stress-induced production of ceramide, and it plays an important role in cell-cycle arrest, apoptosis, inflammation, and eukaryotic stress responses. Recent studies have identified a small region at the very N-terminus of the 55 kDa tumour necrosis factor receptor (TNF-R55), designated the neutral sphingomyelinase activating domain (NSD) that is responsible for the TNF-induced activation of N-SMase. There is no direct association between TNF-R55 NSD and N-SMase; instead, a protein named factor associated with N-SMase activation (FAN) has been reported to couple the TNF-R55 NSD to N-SMase. Since the th... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217434 Wed, 14 Sep 2011 08:48:02 +0100 5217434 http://www.medworm.com/index.php?rid=5217433&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904435%26dopt%3DAbstract Authors: Kumar S Abstract GAGA factor (GAF) is involved in both gene activation and gene repression and plays a role in the modulation of chromatin structure. In Drosophila, Trithroax like (Trl) gene encodes the DNA binding protein called GAGA factor (GAF). Trl-GAF binds to GAGA sites through its C2H2 zinc finger domain and has an N-terminal BTB/POZ domain. Identification of Trl-GAF homologue in mouse helps in deeper understanding of the mechanism and function. Conventional alignment tools such as BLAST and FASTA cannot identify homologues in mouse genome as their sequence identity is below 30%. In the present study, various sequence and structure analyses were followed for the detection of remote homologues of Drosophila GAGA FACTOR in mouse to identify as Zbtb3. Through homology ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217433 Wed, 14 Sep 2011 08:48:02 +0100 5217433 http://www.medworm.com/index.php?rid=5217432&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904436%26dopt%3DAbstract In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method. PMID: 21904436 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217432 Wed, 14 Sep 2011 08:48:02 +0100 5217432 http://www.medworm.com/index.php?rid=5217431&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904437%26dopt%3DAbstract We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm. AVAILABILITY: The database is available for free at http://code.google.com/p/valfold/ PMID: 21904437 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217431 Wed, 14 Sep 2011 08:48:02 +0100 5217431 http://www.medworm.com/index.php?rid=5217430&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904438%26dopt%3DAbstract Authors: Ganguli S, Mitra S, Datta A Abstract The accurate prediction of a comprehensive set of messenger putative antagomirs against microRNAs (miRNAs) remains an open problem. In particular, a set of putative antagomirs against human miRNA is predicted in this current version of database. We have developed Antagomir database, based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA dataset was used as template to design putative antagomirs, using GC content and secondary structures as parameters. The algorithm used predicted the free energy of unbound antagomirs. Although in its infancy the development of antagomirs, that can target cell specific genes or families of genes, may pave the way forward for the generation of a new class of therapeutics, to treat ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217430 Wed, 14 Sep 2011 08:48:02 +0100 5217430 http://www.medworm.com/index.php?rid=5217429&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904439%26dopt%3DAbstract Authors: Yao JQ, Yu F Abstract Digital expression (DE) is an important application of RNA-seq technology to quantify the transcriptome. The number of mapped reads to each transcript or gene varies under different conditions and replicates. Currently, three different statistical algorithms (edgeR, DESeq and bayseq) are available as R packages, to compare the reads to identify significantly expressed transcripts or genes. So far, users have to manually install and run each R package separately. It is also of users' interest to compare the results of different approaches. Here, we present a pipeline DEB which automates all the steps in file preparation, computation and result comparison. AVAILABILITY: The database is available for free at http://www.ijbcb.org/DEB/php/onlinetool.php. ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5217429 Wed, 14 Sep 2011 08:48:02 +0100 5217429 http://www.medworm.com/index.php?rid=5192371&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21887013%26dopt%3DAbstract Authors: Kumar D, Mittal Y Abstract Lectins, a class of carbohydrate-binding proteins and widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes encompass different members that are diverse in their protein structures, carbohydrate affinities and specificities, their larger biological roles and potential applications. To attain an effective use of all the diverse data initially an animal lectin database 'AnimalLectinDb' with information pertaining to taxonomic, structural, domain architecture, molecular sequence, carbohydrate structure and blood group specificity has been developed. It is expected to be of high value not only for basic study in lectin biology but also for advanced research in pursuing ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5192371 Sun, 04 Sep 2011 09:00:05 +0100 5192371 http://www.medworm.com/index.php?rid=5192370&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21887014%26dopt%3DAbstract Authors: Mishra H, Singh N, Misra K, Lahiri T Abstract Identification of promoter region is an important part of gene annotation. Identification of promoters in eukaryotes is important as promoters modulate various metabolic functions and cellular stress responses. In this work, a novel approach utilizing intensity values of tilling microarray data for a model eukaryotic plant Arabidopsis thaliana, was used to specify promoter region from non-promoter region. A feed-forward back propagation neural network model supported by genetic algorithm was employed to predict the class of data with a window size of 41. A dataset comprising of 2992 data vectors representing both promoter and non-promoter regions, chosen randomly from probe intensity vectors for whole genome of Arabidopsis thal... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5192370 Sun, 04 Sep 2011 09:00:05 +0100 5192370 http://www.medworm.com/index.php?rid=5192369&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21887015%26dopt%3DAbstract Authors: Kim C, Park D, Seol Y, Hahn J Abstract The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage. PMID: 21887015 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5192369 Sun, 04 Sep 2011 09:00:05 +0100 5192369 http://www.medworm.com/index.php?rid=5192368&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21887016%26dopt%3DAbstract Authors: Milev I, Yahubyan G, Minkov I, Baev V Abstract MicroRNAs (miRNAs) are important negative regulators of gene expression in plant and animals, which are endogenously produced from their own genes. Computational comparative approach based on evolutionary conservation of mature miRNAs has revealed a number of orthologs of known miRNAs in different plant species. The homology-based plant miRNA discovery, followed by target prediction, comprises several steps, which have been done so far manually. Here, we present the bioinformatics pipeline miRTour which automates all the steps of miRNA similarity search, miRNA precursor selection, target prediction and annotation, each of them performed with the same set of input sequences. AVAILABILITY: The database is available for free at h... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5192368 Sun, 04 Sep 2011 09:00:05 +0100 5192368 http://www.medworm.com/index.php?rid=5095658&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814388%26dopt%3DAbstract Authors: Sánchez J All coding DNAs exhibit 3-base periodicity (TBP), which may be defined as the tendency of nucleotides and higher order n-tuples, e.g. trinucleotides (triplets), to be preferentially spaced by 3, 6, 9 etc, bases, and we have proposed an association between TBP and clustering of same-phase triplets. We here investigated if TBP was affected by intercodon dinucleotide tendencies and whether clustering of same-phase triplets was involved. Under constant protein sequence intercodon dinucleotide frequencies depend on the distribution of synonymous codons. So, possible effects were revealed by randomly exchanging synonymous codons without altering protein sequences to subsequently document changes in TBP via frequency distribution of distances (FDD) of DNA triplets. A tripa... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095658 Fri, 05 Aug 2011 11:30:05 +0100 5095658 http://www.medworm.com/index.php?rid=5095652&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814389%26dopt%3DAbstract Authors: Azam F, Prasad MV, Thangavel N, Ali HI Computational assessment of the binding interactions of drugs is an important component of computer-aided drug design paradigms. In this perspective, a set of 30 1-(substituted phenyl)-3-(naphtha[1, 2-d] thiazol-2-yl) urea/thiourea derivatives showing antiparkinsonian activity were docked into inhibitor binding cavity of human adenosine A(2A) receptor (AA2AR) to understand their mode of binding interactions in silico. Lamarckian genetic algorithm methodology was employed for docking simulations using AutoDock 4.2 program. The results signify that the molecular docking approach is reliable and produces a good correlation coefficient (r(2) = 0.483) between docking score and antiparkinsonian activity (in terms of % reduction in catalepsy sco... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095652 Fri, 05 Aug 2011 11:30:05 +0100 5095652 http://www.medworm.com/index.php?rid=5095646&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814390%26dopt%3DAbstract Authors: Quiliano M, Gutierrez AH, Gilman RH, López C, Evangelista W, Sotelo J, Sheen P, Zimic M The pncA gene codes the pyrazinamidase of Mycobacterium tuberculosis, which converts pyrazinamide to ammonia and pyrazinoic-acid, the active antituberculous compound. Pyrazinamidase mutations are associated to pyrazinamide-resistant phenotype, however how mutations affect the structure of the pyrazinamidase, and how structural changes affect the enzymatic function and the level of pyrazinamide-resistance is unknown. The structures of mutated pyrazinamidases from twelve Mycobacterium tuberculosis strains and the pyrazinamide-susceptible H37Rv reference strain were modelled using homology modelling and single amino acid replacement. Physical-chemical and structural parameters of each pyrazin... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095646 Fri, 05 Aug 2011 11:30:05 +0100 5095646 http://www.medworm.com/index.php?rid=5095640&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814391%26dopt%3DAbstract We describe the prediction of short interfering RNA (siRNA) as potential therapeutic molecules for the HA (Haemagglutinin) and NA (Neuraminidase) genes. We screened 90,522 siRNA candidates for HA and 13,576 for NA and selected 1006 and 1307 candidates for HA and NA, respectively based on the proportion of viral sequences that are targeted by the corresponding siRNA, with complete matches. Further short listing to select siRNA with no off-target hits, fulfilling all the guidelines mentioned in approach, provided us 13 siRNAs for haemagglutinin and 13 siRNAs for neuraminidase. The approach of finding siRNA using multiple sequence alignments of amino acid sequences has led to the identification of five conserved amino acid sequences, three in hemagglutinin i.e. RGLFGAIAGFIE, YNAELLV and AIAGF... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095640 Fri, 05 Aug 2011 11:30:05 +0100 5095640 http://www.medworm.com/index.php?rid=5095635&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814392%26dopt%3DAbstract Authors: Razmara J, Deris S, Parvizpour S Structural alignment of proteins is widely used in various fields of structural biology. In order to further improve the quality of alignment, we describe an algorithm for structural alignment based on text modelling techniques. The technique firstly superimposes secondary structure elements of two proteins and then, models the 3D-structure of the protein in a sequence of alphabets. These sequences are utilized by a step-by-step sequence alignment procedure to align two protein structures. A benchmark test was organized on a set of 200 non-homologous proteins to evaluate the program and compare it to state of the art programs, e.g. CE, SAL, TM-align and 3D-BLAST. On average, the results of all-against-all structure comparison by the program hav... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095635 Fri, 05 Aug 2011 11:30:05 +0100 5095635 http://www.medworm.com/index.php?rid=5095608&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814393%26dopt%3DAbstract Authors: Saurabh B, Sneha S, Suvidya R, Pramod K, Shailesh B We have explored the possible role of SSR density in genome to generate biological information. In our study, we have checked the SSR (simple sequence repeats) status in virulent and non virulent genes of enteric bacteria to see whether the SSRs distribution contributes to virulence. The genome, plasmid and virulent genes sequences in fasta format were downloaded from NCBI GenBank and VFDB. The sequences were subjected to SSR analysis using software tool ssr.exe. The resulting data was pasted in excel sheet and further analyzed for percentage of each type of SSR. Higher nucleotide repeats have been observed in our study. Overall high density of SSRs can enhance antigenic variance of the pathogen population in a strategy that ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095608 Fri, 05 Aug 2011 11:30:05 +0100 5095608 http://www.medworm.com/index.php?rid=5095593&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814394%26dopt%3DAbstract In this study, we used programming implementations of Python to statistically quantify the representation of glycoproteins by scanning all the available proteome sequence data at ExPASy server for the presence of glycoproteins and also the enzyme which plays critical role in glycosylation i.e. OST. Our results suggest that more than 50% of the proteins carry N-X-S/T motif i.e. they could be potential glycoproteins. Furthermore, approximately 28-36% (1/3) of proteins possesses signature motifs which are characteristic features of enzyme OST. Quantifying this bias individually reveals that both the number of proteins tagged with N-X-S/T motif and the average number of motifs per protein is significantly higher in case of eukaryotes when compared to prokaryotes. In the light of these results ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095593 Fri, 05 Aug 2011 11:30:05 +0100 5095593 http://www.medworm.com/index.php?rid=5095534&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814395%26dopt%3DAbstract In this study, 272 essential proteins were identified out of which 42 proteins were unique to the microorganism. The study identified 15 membrane localized drug targets. Amongst these 15, molecular modeling and structure validation of the five membrane localized drug target proteins could only be achieved because of the low sequence identity of the remaining proteins with RCSB structures. These 3D structures can be further characterized by invitro and invivo studies for the development of novel vaccine epitopes and novel antibiotic therapy against Borrelia burgdorferi. PMID: 21814395 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095534 Fri, 05 Aug 2011 11:30:05 +0100 5095534 http://www.medworm.com/index.php?rid=5095502&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814396%26dopt%3DAbstract Authors: Joshi RK, Kar B, Nayak S Resistance genes are among the most important gene classes for plant breeding purposes being responsible for activation of plant defense mechanisms. Among them, the nucleotide binding site-leucine rich repeat (NBS-LRR) class R-genes are the most abundant and actively found in all types of plants. Insilico characterization of EST database resulted in the detection of 28 NBS types R-gene sequences in Curcuma longa. All the 28 sequences represented the NB-ARC domain, 21 of which were found to have highly conserved motif characteristics and categorized as regular NBS genes. The Open Reading Frames varied from 361 (CL.CON.3566) to 112 (CL.CON.1267) with an average of 279 amino acids. Most alignment occurred with monocots (67.8%) with emphasis on Oryza sativ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095502 Fri, 05 Aug 2011 11:30:05 +0100 5095502 http://www.medworm.com/index.php?rid=5095455&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814397%26dopt%3DAbstract Authors: Sharma S, Biswas S The last decade was taken by storm when the existence of a class of small (˜22nt long) non - coding RNA species, known as microRNAs (miRNAs) came into light. MicroRNAs are one of the most abundant groups of regulatory genes in multicellular organisms and play fundamental roles in many cellular processes. Among these, miRNAs have been shown to prevent cell division and drive terminal differentiation, thus playing a causal role in the generation or maintenance of cancerous tumours. The unique expression profiles of different miRNAs in various types and stages of cancer suggest their performance as novel biomarkers. This discussion focuses on miRNAs implicated in cancer-associated events and strives to re-establish their sequential features which may classify ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5095455 Fri, 05 Aug 2011 11:30:05 +0100 5095455 http://www.medworm.com/index.php?rid=5049310&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738307%26dopt%3DAbstract This article represents inner mitochondrial membrane as a natural superconductor giving also the corresponding mathematical model; nevertheless the creation of electric complexes into the inner mitochondrial membrane due to the unusual concentration of protons disrupts the normal flow of electrons and the production of ATP. Therefore, we propose the term 'electric thromboses' for the explanation of these inadequate electrons' flow, presenting simultaneously a natural mechanism of this important and unique phenomenon. PMID: 21738307 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049310 Fri, 22 Jul 2011 03:13:31 +0100 5049310 http://www.medworm.com/index.php?rid=5049309&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738308%26dopt%3DAbstract Authors: Bala S, Pathak RK, Mishra V The present work delineates the combinatorial approach of firstly, creation of a centralized data-set comprising signalling proteins identified on the basis of altered expression, such as over-expression or repression of a set of signalling protein(s) leading to the cause of the disease, which is based on published reports screened through Pubmed and secondly, in the in silico creation of novel lead (drug) molecules and docking of identified signalling biomarkers using such drugs to investigate possibility of their future application in the model systems eventually. EPAC (Exchange Protein Activated by cAMP) emerges as a signalling biomarker in cases studied presently. Brefeldin, the known inhibitor of EPAC, though the mechanism yet unexplored, has b... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049309 Fri, 22 Jul 2011 03:13:31 +0100 5049309 http://www.medworm.com/index.php?rid=5049308&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738309%26dopt%3DAbstract Authors: Kiran JA, Chakravarthi VP, Kumar YN, Rekha SS, Kruti SS, Bhaskar M Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049308 Fri, 22 Jul 2011 03:13:31 +0100 5049308 http://www.medworm.com/index.php?rid=5049307&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738310%26dopt%3DAbstract We examined each gene for its position in the human genome and found a non-stochastic occurrence for only seven genes, on chromosome 22. Six of the seven genes were identified, CSNK1E (casein kinase 1 epsilon), DGCR8 (Di George syndrome critical region 8), GGA1 (Golgi associated gamma adaptin ear containing ARF binding protein 1), MAPK11 (mitogen activated protein kinase 11), SMCR7L (Smith-Magenis syndrome chromosome region candidate 7-like), andTBC1D22A (TBC1 domain family member 22A). Six genes (CSNK1E, DGCR8, GGA1, MAPK11, SMCR7L, and one unidentified gene) had similar expression profiles across HAD/HIVE, HAD, and HIVE vs. HIV+ whereas one gene (TBC1D22A) had a differing gene expression profile across these patient categories. There are several mental disease-related genes including miR... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049307 Fri, 22 Jul 2011 03:13:31 +0100 5049307 http://www.medworm.com/index.php?rid=5049306&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738311%26dopt%3DAbstract Authors: Senthil R, Angel KJ, Malathi R, Venkatesan D A study about isolation, identification and analysis of bacteria in waste water. Here the tannery effluent used as a sample for the entire analysis. A bacterial strain, designated MPC1 was isolated from a waste water sample collected from tannery effluent, Trichy, India and identified using a molecular approach. On the basis of the bacterial 16s rRNA gene sequence phylogeny and comparison of this gene sequence with sequence in RNA sequence database, it is considered that isolate is closely related to members of the Pseudomonas aeruginosa Sp. Phylogenetic and molecular evolutionary analyses were conducted using MEGA. Identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Pseudomona... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049306 Fri, 22 Jul 2011 03:13:31 +0100 5049306 http://www.medworm.com/index.php?rid=5049305&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738312%26dopt%3DAbstract In this study we carried out the bioinformatics analysis of one of the key enzymes of pgl locus from Campylobacter jejuni, known as PglB, which is distributed widely in bacteria and AglB from archaea. Relatively little sequence similarity was observed in the archaeal AglB(s) as compared to those of the bacterial PglB(s). In addition we tried to the answer the question of as to why not all the sequins Asp-X-Ser/Thr have an equal opportunity to be glycosylated by looking at the influence of the neighboring amino acids but no significant conserved pattern of the flanking sites could be identified. The software tool was developed to predict the potential glycosylation sites in autotransporter protein, the virulence factors of gram negative bacteria, and our results revealed that the frequency ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049305 Fri, 22 Jul 2011 03:13:31 +0100 5049305 http://www.medworm.com/index.php?rid=5049304&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738313%26dopt%3DAbstract Authors: Gupta U, Banerjee K, Gabrani R, Gupta S, Sharma SK, Jain CK The immunosuppressive individuals are highly prone to get afflicted with invasive opportunistic fungal infections such as Candidiasis, Aspergillosis, Histoplasmosis, Coccidioidomycosis, Blastomycosis, Penicilliosis, Cryptococcosis and Zygomycosis which are becoming a cause of concern to the mankind due to their high morbidity and mortality rates. The existing antifungal agents are not completely effective due to their severe side-effects and recurrent drug resistance in fungi. Hence, there is an urgent need to develop newer and better antifungal drugs. The enzyme Glucosamine-6-phosphate (G-6-P) synthase catalyzes the ratelimiting step of the fungal cell-wall biosynthetic pathway and targeting it can inhibit the growth... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049304 Fri, 22 Jul 2011 03:13:31 +0100 5049304 http://www.medworm.com/index.php?rid=5049303&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738314%26dopt%3DAbstract Authors: Kudo Y, Okada Y We apply a combined method of heuristic attribute reduction and evaluation of relative reducts in rough set theory to gene expression data analysis. Our method extracts as many relative reducts as possible from the gene-expression data and selects the best relative reduct from the viewpoint of constructing useful decision rules. Using a breast cancer dataset and a leukemia dataset, we evaluated the classification accuracy for the test samples and biological meanings of the rules. As a result, our method presented superior classification accuracy comparable to existing salient classifiers. Moreover, our method extracted interesting rules including a novel biomarker gene identified in recent studies. These results indicate the possibility that our method can serv... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049303 Fri, 22 Jul 2011 03:13:31 +0100 5049303 http://www.medworm.com/index.php?rid=5049302&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738315%26dopt%3DAbstract Authors: Cao W, Sumikoshi K, Nakamura S, Terada T, Shimizu K Attachment of a myristoyl group to NH(2)-terminus of a nascent protein among protein post-translational modification (PTM) is called myristoylation. The myristate moiety of proteins plays an important role for their biological functions, such as regulation of membrane binding (HIV-1 Gag) and enzyme activity (AMPK). Several predictors based on protein sequences alone are hitherto proposed. However, they produce a great number of false positive and false negative predictions; or they cannot be used for general purpose (i.e., taxon-specific); or threshold values of the decision rule of predictors need to be selected with cautiousness. Here, we present novel and taxon-free predictors based on protein primary structure. To identif... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049302 Fri, 22 Jul 2011 03:13:31 +0100 5049302 http://www.medworm.com/index.php?rid=5049301&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738316%26dopt%3DAbstract Authors: Miele M, Sharma A, Capone F, Raucci R, Guerriero E, Colonna G, Castello G, Stasio MD, Costantini S The cytokines/related receptors system represents a complex regulatory network that is involved in those chronic inflammatory processes which lead to many diseases as cancers. We developed a Cytokine Receptor Database (CytReD) to collect information on cytokine receptors related to their biological activity, gene data, protein structures and diseases in which these and their ligands are implicated. This large set of information may be used by researchers as well as by physicians or clinicians to identify which cytokines, reported in the literature, are important in a given disease and, therefore, useful for purposes of diagnosis or prognostic. AVAILABILITY: The database is availa... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049301 Fri, 22 Jul 2011 03:13:31 +0100 5049301 http://www.medworm.com/index.php?rid=5049300&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738317%26dopt%3DAbstract Authors: Sheoran S, Pandey B, Singh R, Sharma P, Chatrath R Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn(III) at the active site. Therefore, it is of interest to study MnSOD from bread wheat (a grain crop). However, a structure model is not yet solved for bread wheat MnSOD. Hence, we describe the structure model of bread wheat MnSOD developed using homology model. The model provides molecular insight to metal binding molecular function towards the understanding of oxidative stress resistance in plants. The distinction of bread wheat (a monocot) MnSOD from dicots is also shown using phylogenetic analysis. PMID: 21738317 [PubMed] (Source: Bioinfo... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049300 Fri, 22 Jul 2011 03:13:31 +0100 5049300 http://www.medworm.com/index.php?rid=5049299&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738318%26dopt%3DAbstract The objective of this study was the construction of novel transformation vectors for PATE gene silencing. Six different transformation vectors targeted against PATE gene were constructed using 619 bp long PATE gene (5' region) fragment (from GenBank AF507115). In one set of three transformation vectors, PATE gene fragment was fused with CaMV 35S promoter in antisense, intron-spliced inverted repeat (ISIR), and inverted repeat (IR) orientations to generate antisense mRNA and hair-pin RNAs (hpRNA). In another set of three transformation vectors with same design, CaMV 35S was replaced with Oil palm mesocarp tissue-specific promoter (MSP). The expression cassette of antisense, ISIR, and IR of PATE gene fragments were constructed in primary cloning vector, pHANNIBAL or its derivative/s. Finally... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049299 Fri, 22 Jul 2011 03:13:31 +0100 5049299 http://www.medworm.com/index.php?rid=5049298&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738319%26dopt%3DAbstract Authors: Ishikawa Y, Fujii S Influenza is a yearly seasonal threat and major cause of mortality, particularly in children and the elderly. Although neuraminidase inhibitors and M2 protein blockers are used for medication, drug resistance has gradually emerged. Thus, the development of effective anti-influenza drugs targeting different constituent proteins of the virus is urgently desired. In this light, we carried out molecular docking to predict the binding modes of anti-influenza diketo acid inhibitors in the active site of the PAN subunit of the metalloenzyme RNA polymerase of influenza virus. The calculations suggested that the dianionic forms of the diketo acids should chelate the dinuclear manganese center as dinucleating ligands and sequester it. They also indicated that the dik... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049298 Fri, 22 Jul 2011 03:13:31 +0100 5049298 http://www.medworm.com/index.php?rid=5049297&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738320%26dopt%3DAbstract Authors: Pitchai D, Manikkam R, V SL, Singaram R Design of potential drug-like candidates for cancer is of interest in recent years. We used 60 compounds which are known to have the potential to down regulate Nuclear Factor kappaB (NFκB) for this study. The compounds were assessed for Lipinski's RO5 and ADMET properties. Allixin, anethole, capsaicin, linearol and syringic acid satisfied both Lipinski's RO5 and ADMET properties. These compounds showed strong molecular interaction with receptor GPCR55 indicating they have ability to block GPCR55. Thus, their role in anticellular proliferation and induction of apoptosis is implied. PMID: 21738320 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049297 Fri, 22 Jul 2011 03:13:31 +0100 5049297 http://www.medworm.com/index.php?rid=5049296&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738321%26dopt%3DAbstract Authors: Paris D, Mathura V, Ait-Ghezala G, Beaulieu-Abdelahad D, Patel N, Bachmeier C, Mullan M Alzheimer's disease (AD) is characterized by the brain accumulation of Aβ peptides and by the presence of neurofibrillary tangles. Aβ is believed to play an important role in AD and it has been shown that certain flavonoids can affect Aβ production. Recently, it was suggested that the Aβ lowering properties of flavonoids are mediated by a direct inhibition the β-secretase (BACE-1) activity, the rate limiting enzyme responsible for the production of Aβ peptides. Westernblots and ELISAs were employed to monitor the impact of flavonoids on amyloid precursor protein processing and Aβ production. A cell free chemoluminescent assay using human recombinant BACE-1 was used to assess the effe... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049296 Fri, 22 Jul 2011 03:13:31 +0100 5049296 http://www.medworm.com/index.php?rid=5049295&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738322%26dopt%3DAbstract Authors: Iqbal S, Masood K, Jafer O Two types of antiviral treatments, namely, interferon and nucleoside/nucleotide analogues are available for hepatitis infections. The selection of drug and dose determined using known pharmacokinetics and pharmacodynamics data is important. The lack of sufficient information for pharmacokinetics of a drug may not produce the desired results. Artificial neural network (ANN) provides a novel model-independent approach to pharmacokinetics and pharmacodynamics data. ANN model is created by supervised learning of 90 patients sample to predict the treatment strategy (lamivudine only and Lamivudine + Interferon) on the basis of viral load, liver function test, visit number, treatment duration, ethnic area, sex, and age. The model was trained with 68 (77.3%)... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049295 Fri, 22 Jul 2011 03:13:31 +0100 5049295 http://www.medworm.com/index.php?rid=5049294&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738323%26dopt%3DAbstract Authors: Polak S, Wisniowska B, Fijorek K, Glinka A, Polak M, Mendyk A Drug cardiotoxicity is one of the main reasons of fatal drug related problem events and the subsequent withdrawals. Therefore, its early assessment is a crucial element of the drug development process. For the drug driven hERG inhibition assessment, which is assumed to be the main reason for toxicity, in vitro techniques are used. Gold standards are based on the Patch Clamp method with the use of various cell models but due to its low throughput, insilico models have become more appreciated. To develop a reliable empirical QSAR model, wide dataset containing a variety of cases has to be available. In this article, a freely available for download, set of data is described. It is based on literature peer-reviewed repo... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049294 Fri, 22 Jul 2011 03:13:31 +0100 5049294 http://www.medworm.com/index.php?rid=5049293&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738324%26dopt%3DAbstract Authors: Subazini TK, Kumar GR Aspergillus terreus is a filamentous ascomycota, which is prominent for its production of lovastatin, an antihypercholesterolemic drug. The commercial importance of lovastatin with annual sales of billions of dollars made us to focus on lovastatin biosynthetic cluster proteins. The analysis of these lovastatin biosynthetic cluster proteins with different perspectives such as physicochemical property, structure based analysis and functional studies were done to find out the role and function of every protein involved in the lovastatin biosynthesis pathway. Several computational tools are used to predict the physicochemical properties, secondary structural features, topology, patterns, domains and cellular location. There are 8 unidentified proteins in lova... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049293 Fri, 22 Jul 2011 03:13:31 +0100 5049293 http://www.medworm.com/index.php?rid=5049292&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738325%26dopt%3DAbstract Authors: Misra N, Panda PK, Shah K, Sukla LB, Chaubey P Although the concept of Reverse Vaccinology was first pioneered for sepsis and meningococcal meningitidis causing bacterium, Neisseria meningitides, no broadly effective vaccine against serogroup B meningococcal disease is yet available. In the present investigation, HLA distribution analysis was undertaken to select three most promiscuous T-cell epitopes out of ten computationally validated epitopes of Iron acquisition proteins from Neisseria MC58 by using the population coverage tool of Immune Epitope Database (IEDB). These epitopes have been determined on the basis of their binding ability with maximum number of HLA alleles along with highest population coverage rate values for all the geographical areas studied. The comparativ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049292 Fri, 22 Jul 2011 03:13:31 +0100 5049292 http://www.medworm.com/index.php?rid=5049291&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738326%26dopt%3DAbstract This study has investigated the effects of naturally occurring nonprotein compounds berberine and monocaffeyltartaric acid that inhibits 5-α reductase type 2. Our results reveal that these compounds use less energy to bind to 5-α reductase and inhibit its activity. Their high ligand binding affinity to 5-α reductase introduces the prospect for their use in chemopreventive applications. In addition, they are freely available natural compounds that can be safely used to prevent prostate cancer. PMID: 21738326 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049291 Fri, 22 Jul 2011 03:13:31 +0100 5049291 http://www.medworm.com/index.php?rid=5049290&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738327%26dopt%3DAbstract Authors: Shil P, Chavan S, Cherian S The emergence of new strains of Influenza virus have caused several pandemics over the last hundred years with the latest being the H1N1 Swine flu pandemic of 2009. The Hemagglutinin (HA) protein of the Influenza virus is the primary target of human immune system and is responsible for generation of protective antibodies in humans. Mutations in this protein results in change in antigenic regions (antigenic drift) which consequently leads to loss of immunity in hosts even in vaccinated population (herd immunity). This necessitates periodic changes in the Influenza vaccine composition. In this paper, we investigate the molecular basis of the reported loss of herd immunity in vaccinated population (vaccine component: Influenza A/X-31/1968 (H3N2)) which... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049290 Fri, 22 Jul 2011 03:13:31 +0100 5049290 http://www.medworm.com/index.php?rid=5049289&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738328%26dopt%3DAbstract This study demonstrated that B cell and T cell predicted epitopes from TSOL18 were not able to completely protect pigs against an oral challenge with Taenia solium proglottids. Therefore, other linear epitopes or eventually conformational epitopes may be responsible for the protection conferred by TSOL18. PMID: 21738328 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049289 Fri, 22 Jul 2011 03:13:31 +0100 5049289 http://www.medworm.com/index.php?rid=5049288&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738329%26dopt%3DAbstract Authors: Shashidharan A, Singh R, Bhasker S, Mohankumar C The Bos indicus Vechur breed cow milk is known for its medicinal value and the breed is listed under the category of critically maintained breeds by the Food and Agriculture Organization. The lactoferrin protein in milk is known for its nutritional value. Gene polymorphisms have been reported for Bovine lactoferrin. Mutations in the evolutionarily conserved sites tend to impair protein function and are related with the physicochemical difference between the known variants with 11 SNPs within the wild type. Structural differences are located due to these SNPs that may lead to functional variations. The structural variation is seen primarily in the first 48 residues at 5' end in all the samples modelled. Out of 11 SNPs 5 amino aci... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049288 Fri, 22 Jul 2011 03:13:31 +0100 5049288 http://www.medworm.com/index.php?rid=5049287&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738330%26dopt%3DAbstract In this study, we propose an enhanced algorithm that provides stability and robustness in identifying differentially expressed genes in an expression profile analysis. Our proposed algorithm uses multiple clustering algorithms under the consensus clustering framework. The results of the experiment show that the robustness of our method provides a consistent structure of clusters, similar to the structure found in the previous study. Furthermore, our algorithm outperforms any single clustering algorithms in terms of the cluster quality score. PMID: 21738330 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049287 Fri, 22 Jul 2011 03:13:31 +0100 5049287 http://www.medworm.com/index.php?rid=5049286&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738331%26dopt%3DAbstract Authors: Sankar S, Kuppanan S, Balakrishnan B, Nandagopal B The IS6110 belongs to the family of insertion sequences (IS) of the IS3 category. This insertion sequence was reported to be specific for Mycobacterium tuberculosis complex and hence is extensively exploited for laboratory detection of the agent of tuberculosis and for epidemiological investigations based on polymerase chain reaction. IS6110 is 1361-bp long and within this sequence different regions have been utilized as targets in the identification of M. tuberculosis by PCR. However, the results are not always consistent, specific and sensitive. In recent years, a few clinical investigations raised concerns over IS6110 specificity and sensitivity in the diagnosis of tuberculosis due to false-positive (homology with other tar... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049286 Fri, 22 Jul 2011 03:13:31 +0100 5049286 http://www.medworm.com/index.php?rid=5049285&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738332%26dopt%3DAbstract Authors: Samantaray SD, Singh P, Suresh BV, Sharma S, Taj G, Kumar A MAPK (Mitogen Activated Protein Kinase) is a Ser/Thr kinase, which plays a crucial role in plant growth and development, transferring the extra cellular stimuli into intracellular response etc. Manual identification of these MAPK in the plant genome is tedious and time taking process. There are number of online servers which predict the P-site (phosphorylation site), find the motifs and domain but there is no specific tool which can identify all them together. In order to identify the P-Site, phosphorylation site consensus sequences and domain of the MAPK in plant genome, we developed a tool, MAP Kinase analyzer. MAP kinase analyzer take protein sequence as input in the fasta format and the output of tool includes: 1)... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049285 Fri, 22 Jul 2011 03:13:31 +0100 5049285 http://www.medworm.com/index.php?rid=5049284&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21738333%26dopt%3DAbstract Authors: Srivastava AK, Sahni NS Ontologies have emerged as a fast growing research topic in the area of semantic web during last decade. Currently there are 204 ontologies that are available through OBO Foundry and BioPortal. Several excellent tools for navigating the ontological structure are available, however most of them are dedicated to a specific annotation data or integrated with specific analysis applications, and do not offer flexibility in terms of general-purpose usage for ontology exploration. We developed OntoVisT, a web based ontological visualization tool. This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049284 Fri, 22 Jul 2011 03:13:31 +0100 5049284 http://www.medworm.com/index.php?rid=5049282&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769187%26dopt%3DAbstract Authors: Rajasekaran E, Akila K, Vijayasarathy M Sequence stretches in proteins that do not fold into a form are referred as disordered regions. Databases like Disport describe disordered regions in proteins and web servers like PrDOS and DisEMBL, facilitate the prediction of disordered regions. These studies are often based on residue level features. Here, we describe proteins with disordered regions using carbon content and distributions. The distribution pattern for proteins with disordered regions is different from those that do not show disordered regions. PMID: 21769187 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049282 Fri, 22 Jul 2011 03:13:31 +0100 5049282 http://www.medworm.com/index.php?rid=5049279&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769188%26dopt%3DAbstract We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism's biology and may play a role in pathogenesis. PMID: 21769188 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049279 Fri, 22 Jul 2011 03:13:31 +0100 5049279 http://www.medworm.com/index.php?rid=5049278&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769189%26dopt%3DAbstract We describe the analysis of prediction data in a sequence dataset of hypothetical protein orthologs of Pongo abelii (orangutan) and Sus scrofa (pig). It should be noted that these orangutan-pig orthologs are also non-homologous to human proteins. These predicted data find application in the genome wide annotation of proteins in poorly understood genomes. ABBREVIATIONS: PDB - Protein Data Bank, DEG - Database of Essential Genes, CDD - Conserved Domain Database, IUCN - International Union for Conservation of Nature. PMID: 21769189 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049278 Fri, 22 Jul 2011 03:13:31 +0100 5049278 http://www.medworm.com/index.php?rid=5049276&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769190%26dopt%3DAbstract Authors: Marchewka D, Banach M, Roterman I The characteristic distribution of non-binding interactions in a protein is described. It establishes that hydrophobic interactions can be characterized by suitable 3D Gauss functions while electrostatic interactions generally follow a random distribution. The implementation of this observation suggests differentiated optimization procedure for these two types of interactions. The electrostatic interaction may follow traditional energy optimization while the criteria for convergence shall measure the accordance with 3-D Gauss function. PMID: 21769190 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049276 Fri, 22 Jul 2011 03:13:31 +0100 5049276 http://www.medworm.com/index.php?rid=5049275&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769191%26dopt%3DAbstract Authors: Kannappan P, Narayanan S Yellow fever virus is the causative agent of Yellow fever. The genome of the virus contains three structural and seven non-structural proteins. Of these seven nonstructural proteins, NS2B-NS3 protein complex has protease activity required for viral replication. Predicting the 3D structure of this complex and studying the interaction of residues at the recognized catalytic triad of the complex is an integral part to understand the virus replication mechanism. In the present study, the structure was determined for NS2B-NS3 complex by Homology modeling and modeled structure was validated for its stability. Mutation studies at the residues His94, Asp118 and Ser176 revealed that Asp118-His94 bond played an important role in the structural stability of NS2B-... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049275 Fri, 22 Jul 2011 03:13:31 +0100 5049275 http://www.medworm.com/index.php?rid=5049273&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769192%26dopt%3DAbstract In this study, we have predicted a theoretical structural model for C-terminal domain of CssA by homology modelling using protein data bank (PDB) file, 1NTY-A as template (66.67% sequence identity) in Discovery Studio. The structural model of N-terminal region of Fn was also determined by homology modelling using PDB files 1FBR and 1E88 as templates. The structure of the model was also validated by Ramachandran plot. The energy minimization for Fn was performed in standard dynamic cascade using Steepest Descent algorithm followed by Adopted Basis NR algorithm in Discovery studio. The docking model between C-terminal domain and fibronectin were generated by using ClusPro algorithm. This docking study would be help for better understanding how CS6 interacts with fibronectin of intestinal ext... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049273 Fri, 22 Jul 2011 03:13:31 +0100 5049273 http://www.medworm.com/index.php?rid=5049270&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769193%26dopt%3DAbstract Authors: Kumar PS, Pulicherla K, Ghosh M, Kumar A, Rao KS Enzymes from psychrophiles catalyze the reactions at low temperatures with higher specific activity. Among all the psychrophilic enzymes produced, cold active β-galactosidase from marine psychrophiles revalorizes a new arena in numerous areas at industrial level. The hydrolysis of lactose in to glucose and galactose by cold active β-galactosidase offers a new promising approach in removal of lactose from milk to overcome the problem of lactose intolerance. Herein we propose, a 3D structure of cold active β-galactosidase enzyme sourced from Pseudoalteromonas haloplanktis by using Modeler 9v8 and best model was developed having 88% of favourable region in ramachandran plot. Modelling was followed by docking studies with the hel... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049270 Fri, 22 Jul 2011 03:13:31 +0100 5049270 http://www.medworm.com/index.php?rid=5049267&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769194%26dopt%3DAbstract Authors: Roy S, Maheshwari N, Chauhan R, Sen NK, Sharma A Various species of Ocimum have acquired special attention due to their medicinal properties. Different parts of the plant (root, stem, flower, leaves) are used in the treatment of a wide range of disorders from centuries. Experimental structures (X-ray and NMR) of proteins from different Ocimum species, are not yet available in the Protein Databank (PDB). These proteins play a key role in various metabolic pathways in Ocimum. 3D structures of the proteins are essential to determine most of their functions. Homology modeling approach was employed in order to derive structures for these proteins. A program meant for comparative modeling- Modeller 9v7 was utilized for the purpose. The modeled proteins were further validated by Proc... Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049267 Fri, 22 Jul 2011 03:13:31 +0100 5049267 http://www.medworm.com/index.php?rid=5049264&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769195%26dopt%3DAbstract This study demonstrates that the circumsporozoite protein of Plasmodium falciparum shows similarity with Plasmodium cynomolgi and Plasmodium knowlesi. The merozoite surface protein-1 of Plasmodium coatneyi forms a monophyletic group with Plasmodium knowlesi, demonstrating their close relationship and these two species also reveal similarity between the human malaria Plasmodium vivax. This Plasmodium phylogenetic arrangement is evidently crucial to identify shared derived characters as well as particular adaptation of plasmodium species from inside and between monophyletic groups. PMID: 21769195 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049264 Fri, 22 Jul 2011 03:13:31 +0100 5049264 http://www.medworm.com/index.php?rid=5049261&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21769196%26dopt%3DAbstract Authors: Sharma OP, Jadhav A, Hussain A, Kumar MS Viral Protein Database is an interactive database for three dimensional viral proteins. Our aim is to provide a comprehensive resource to the community of structural virology, with an emphasis on the description of derived data from structural biology. Currently, VPDB includes ˜1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search. Interactivity has been enhanced by using Jmol, WebMol and Strap to visualize the viral protein molecular structure. AVAILABILITY: The database is available for free at http://www.vpdb.bicpu.edu.in. PMID: 21769196 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=5049261 Fri, 22 Jul 2011 03:13:31 +0100 5049261 http://www.medworm.com/index.php?rid=4855468&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572879%26dopt%3DAbstract Authors: Sowmya G, Anita S, Kangueane P Protein heterodimer complexes are often involved in catalysis, regulation, assembly, immunity and inhibition. This involves the formation of stable interfaces between the interacting partners. Hence, it is of interest to describe heterodimer interfaces using known structural complexes. We use a non-redundant dataset of 192 heterodimer complex structures from the protein databank (PDB) to identify interface residues and describe their interfaces using amino-acids residue property preference. Analysis of the dataset shows that the heterodimer interfaces are often abundant in polar residues. The analysis also shows the presence of two classes of interfaces in heterodimer complexes. The first class of interfaces (class A) with more polar residues tha... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855468 Tue, 24 May 2011 21:00:02 +0100 4855468 http://www.medworm.com/index.php?rid=4855467&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572880%26dopt%3DAbstract Authors: Danishuddin M, Chatrath R, Singh R Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis dep... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855467 Tue, 24 May 2011 21:00:02 +0100 4855467 http://www.medworm.com/index.php?rid=4855466&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572881%26dopt%3DAbstract Authors: Rajarajan S, Ibrahim KS, Pandian SK Inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. After their discovery, inteins have been quickly identified in organisms from all three kingdoms of life - eucarya, bacteria and archaea, but their distribution is sporadic. Here we report the identification and bioinformatics characterization of intein in DNA polymerase A gene of bacteriophage APSE (Acyrthosiphon pisum Secondary Endosymbiont bacteriophage) infecting the Aphid secondary endosymbionts of eukaryotic insects such as Acyrthosiphon pisum, Uroleucon rudbeckiae. The insertion site of intein within APSE family A DNA polymerase extein was identified to be dpola. Hence we propose this as a unique intein of family A ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855466 Tue, 24 May 2011 21:00:02 +0100 4855466 http://www.medworm.com/index.php?rid=4855465&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572882%26dopt%3DAbstract Authors: Biswas S, Manikandan J, Pushparaj PN Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease of unidentified aetiology, chiefly affecting the synovial membranes of joints, cartilage, bone, bursa and tendon sheath. Osteoarthritis (OA) is a degenerative disorder and encompass different sets of pathogenic pathways than RA; however, it shows a medley of clinical manifestations or symptoms resembling RA. Hence, we intend to identify more disease specific biomarkers through the meta-analysis of microarray datasets that can be crucial in the differential diagnosis, disease specific treatment as well as management of both RA and OA in a typical clinical setting. PMID: 21572882 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855465 Tue, 24 May 2011 21:00:02 +0100 4855465 http://www.medworm.com/index.php?rid=4855464&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572883%26dopt%3DAbstract Authors: Mishra H, Lahiri T Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as protein marker. The protocol used multiple ILMFD inputs obtained for a protein to produce a set of mapped outputs as possible SRI candidates. The outputs were further clustered and largest cluster centre after normalization was found to be a close approximation of expec... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855464 Tue, 24 May 2011 21:00:02 +0100 4855464 http://www.medworm.com/index.php?rid=4855463&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572884%26dopt%3DAbstract Authors: Alexiou A, Vlamos P In general RNA prediction problem includes genetic mapping, physical mapping and structure prediction. The ultimate goal of structure prediction is to obtain the three dimensional structure of bimolecules through computation. The key concept for solving the above mentioned problem is the appropriate representation of the biological structures. Even though, the problems that concern representations of certain biological structures like secondary structures either are characterized as NP-complete or with high complexity, few approximation algorithms and techniques had been constructed, mainly with polynomial complexity, concerning the prediction of RNA secondary structures. In this paper, a new class of Motzkin paths is introduced, the so-called semi-elevated... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855463 Tue, 24 May 2011 21:00:02 +0100 4855463 http://www.medworm.com/index.php?rid=4855462&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572885%26dopt%3DAbstract Authors: Yuniarti N, Ikawati Z, Istyastono EP Structure-based virtual screening (SBVS) protocols were developed to find cyclooxygenase-2 (COX-2) inhibitors using the Protein-Ligand ANT System (PLANTS) docking software. The directory of useful decoys (DUD) dataset for COX-2 was used to retrospectively validate the protocols; the DUD consists of 426 known inhibitors in 13289 decoys. Based on criteria used in the article describing DUD datasets, the default protocol showed poor results. However, having ARG513 as a hydrogen bond anchor increased the quality of the SBVS protocol. The modified protocol showed results that could be well considered, with a maximum enrichment factor (EF(max)) value of 32.2. PMID: 21572885 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855462 Tue, 24 May 2011 21:00:02 +0100 4855462 http://www.medworm.com/index.php?rid=4855461&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572886%26dopt%3DAbstract Authors: Daisy P, Singh SK, Vijayalakshmi P, Selvaraj C, Rajalakshmi M, Suveena S Pharmacophore feature is defined by a set of chemical structure patterns having the active site of drug like molecule. Pharmacophore can be used to assist in building hypothesis about desirable chemical properties in drug molecule and hence it can be used to refine and modify drug candidates. We predicted the pharmacophoric features of 150 medicinal compounds from plants for anti-cancer, anti-carcinogenic, anti-diabetic, anti-microbial, and anti-oxidant. Estimation of pharmacophoric feature is necessary to ensure the optimal supramolecular interaction with a biological target and to trigger or block its biological response. We subsequently make this data available to open access using a database at the UR... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855461 Tue, 24 May 2011 21:00:02 +0100 4855461 http://www.medworm.com/index.php?rid=4855460&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572887%26dopt%3DAbstract Authors: Gadewal NS, Zingde SM The oral cancer gene database has been compiled to enable fast retrieval of updated information and role of the genes implicated in oral cancer. The first version of the database with 242 genes was published in Online Journal of Bioinformatics 8(1), 41-44, 2007. In the second version, the database has been enlarged to include 374 genes by adding 132 gene entries. The architecture and format of the database is similar to the earlier version, and includes updated information and external hyperlinks for all the genes. The functional gene interaction network for important biological processes and molecular functions has been rebuilt based on 374 genes using 'String 8.3'. The database is freely available at http://www.actrec.gov.in/OCDB/index.htm and provides ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855460 Tue, 24 May 2011 21:00:02 +0100 4855460 http://www.medworm.com/index.php?rid=4855459&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572888%26dopt%3DAbstract Authors: Chen M, Tan Z, Zeng G Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid. PMID: 21572888 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855459 Tue, 24 May 2011 21:00:02 +0100 4855459 http://www.medworm.com/index.php?rid=4855458&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584183%26dopt%3DAbstract Authors: Selvaraj S, Natarajan J Microarrays are one of the latest breakthroughs in experimental molecular biology that allow monitoring the expression levels of tens of thousands of genes simultaneously. Arrays have been applied to studies in gene expression, genome mapping, SNP discrimination, transcription factor activity, toxicity, pathogen identification and many other applications. In this paper we concentrate on discussing various bioinformatics tools used for microarray data mining tasks with its underlying algorithms, web resources and relevant reference. We emphasize this paper mainly for digital biologists to get an aware about the plethora of tools and programs available for microarray data analysis. First, we report the common data mining applications such as selecting dif... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855458 Tue, 24 May 2011 21:00:02 +0100 4855458 http://www.medworm.com/index.php?rid=4855457&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584184%26dopt%3DAbstract In this study we have demonstrated the inhibition of the 3 selected targets by the two bioactive compounds from marine actinomycetes through in-silico docking studies. Furthermore molecular dynamics simulation were also been performed to check the stability and the amino acids interacted with the 3 molecular targets (EphA2 receptor, EGFR, EGFRvIII) for GBM. Our results suggest that Tetracinomycin D and Chartreusin are the novel and potential inhibitor for the treatment of GBM. PMID: 21584184 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855457 Tue, 24 May 2011 21:00:02 +0100 4855457 http://www.medworm.com/index.php?rid=4855456&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584185%26dopt%3DAbstract Authors: Sinha S, Sundaram S, Kumar V, Tripathi A Visceral Leishmaniasis is a macrophage associated disorder for the treatment of which antimony based drugs like SAG and SSG were the first choice in the recent past. The clinical value of antimony therapy is now declined against VL because increasing cases of Sodium Antimony Gluconate (SAG) resistance have reached outstanding proportion in Bihar, India. Within this context we looked into the protein sequences of ABC transporters of Leishmania spp associated with Visceral Leishmaniasis that are known to play a crucial role in the development of multidrug resistance (MDR). Our studies consisting of ClustalW, Phylogeny and TCOFFEE have pinpointed that ABC transporters have enormously diverged during the process of evolution even within the... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855456 Tue, 24 May 2011 21:00:02 +0100 4855456 http://www.medworm.com/index.php?rid=4855455&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584186%26dopt%3DAbstract Authors: Kumar SD, Krishnamurthy K, Manikandan J, Pakeerappa PN, Pushparaj PN Recruitment of leukocytes circulating in our blood to the sites of infection or tissue damage is the key phenomenon in the acute inflammatory response(s). Among the leukocytes, neutrophils are primarily recruited into the areas of acute inflammation. When neutrophils interact with activated endothelium of the blood vessels, they become migratory and cross the endothelial layer of the blood vessel wall in a process called as leukocyte extravasation. Identifying and understanding the gene regulation of this extravasation phenomenon is one of the key objective of biomedical research aimed at ameliorating or alleviating the symptoms of various diseases, such as rheumatoid arthritis, asthma, anaphylaxis, atheroscl... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855455 Tue, 24 May 2011 21:00:02 +0100 4855455 http://www.medworm.com/index.php?rid=4855454&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584187%26dopt%3DAbstract Authors: Kherraz K, Kherraz K, Kameli A Nitrogen is one of the major growth-limiting nutrients for plants: The main source of nitrogen in most of the higher plants is nitrate taken up through roots. Nitrate can be reduced both in the chloroplasts (photosynthetic tissues) and in proplastes (nonphotosynthetic tissues) such as roots. Ferredoxin-nitrite reductase (NiR) catalyses the reduction of nitrite to ammonium in the second step of the nitrate- assimilation pathway. Homology model of Ferredoxin-nitrite reductase has been constructed using the X-ray structure (PDB code: 2akj) a s a template and MODELLER 9v5 software. The resulting model assessed by PROCHECK, PROSAII and RMSD that showed the final refined model is reliable: has 81% of amino acid sequence identity with template, 0.2Å a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855454 Tue, 24 May 2011 21:00:02 +0100 4855454 http://www.medworm.com/index.php?rid=4855453&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584188%26dopt%3DAbstract Authors: Pihur V, Datta S, Datta S We start by constructing gene-gene association networks based on about 300 genes whose expression values vary between the groups of CFS patients (plus control). Connected components (modules) from these networks are further inspected for their predictive ability for symptom severity, genotypes of two single nucleotide polymorphisms (SNP) known to be associated with symptom severity, and intensity of the ten most discriminative protein features. We use two different network construction methods and choose the common genes identified in both for added validation. Our analysis identified eleven genes which may play important roles in certain aspects of CFS or related symptoms. In particular, the gene WASF3 (aka WAVE3) possibly regulates brain cytokines i... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855453 Tue, 24 May 2011 21:00:02 +0100 4855453 http://www.medworm.com/index.php?rid=4855452&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584189%26dopt%3DAbstract Authors: Vijayan M, Chandrika SK, Vasudevan SE PKSIIIexplorer, a web server based on 'transductive Support Vector Machine' allows fast and reliable prediction of Type III polyketide synthase proteins. It provides a simple unique platform to identify the probability of a particular sequence, being a type III polyketide synthases or not with moderately high accuracy. We hope that our method could serve as a useful program for the type III polyketide researchers. The tool is available at "http://type3pks.in/tsvm/pks3". ABBREVIATIONS: PKS - Polyketide synthase, CHS - Chalcone synthase, SVM - Support vector machine, MCC - Matthews Correlation Coefficient. PMID: 21584189 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855452 Tue, 24 May 2011 21:00:02 +0100 4855452 http://www.medworm.com/index.php?rid=4855451&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584190%26dopt%3DAbstract Authors: Adinarayana KP, Sravani TS, Hareesh C Assigning functions to proteins of unknown function is of considerable interest to the proteomic researchers as the genes encoding them are conserved over various species. Here, we describe HypoDB, a database of hypothetical genes and proteins in six eukaryotes. The database was collected and organized based on the number of entries in each chromosome with few annotations. Hypothetical protein database contains information related to gene and protein sequences, chromosome number and location, secondary and tertiary structure related data. AVAILABILITY: The database is available for free at http://www.trimslabs.com/database/hypodb/index.html. PMID: 21584190 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855451 Tue, 24 May 2011 21:00:02 +0100 4855451 http://www.medworm.com/index.php?rid=4855450&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584191%26dopt%3DAbstract Authors: Jena L, W.hade G, Kumar S, Harinath BC The Mycobacterium tuberculosis Proteome Comparison Database (MTB-PCDB) is an online database providing integrated access to proteome sequence comparison data for five strains of Mycobacterium tuberculosis (H37Rv, H37Ra, CDC 1551, F11 and KZN 1435) sequenced completely so far. MTB-PCDB currently hosts 40252 protein sequence comparison data obtained through inter-strain proteome comparison of five different strains of MTB. 2373 proteins were found to be identical in all 5 strains using MTB H(37)Rv as reference strain. To enable wide use of this data, MTB-PCDB provides a set of tools for searching, browsing, analyzing and downloading the data. By bringing together, M. tuberculosis proteome comparison among virulent & avirulent strains an... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4855450 Tue, 24 May 2011 21:00:02 +0100 4855450 http://www.medworm.com/index.php?rid=4802487&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544164%26dopt%3DAbstract Authors: Sowmya G, Shamini G, Anita S, Sakharkar M, Mathura V, Rodriguez H, Levine AJ, Singer E, Commins D, Somboonwit C, Sinnott JT, Sidhu HS, Rajaseger G, Pushparaj PN, Kangueane P, Shapshak P The human immunodeficiency virus type-1 (HIV-1) gp160 (gp120-gp41 complex) trimer envelope (ENV) protein is a potential vaccine candidate for HIV/AIDS. HIV-1 vaccine development has been problematic and charge polarity as well as sequence variation across clades may relate to the difficulties. Further obstacles are caused by sequence variation between blood and brain-derived sequences, since the brain is a separate compartment for HIV-1 infection. We utilize a threedimensional residue measure of solvent exposure, accessible surface area (ASA), which shows that major segments of gp120 and gp41 k... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802487 Tue, 10 May 2011 06:45:03 +0100 4802487 http://www.medworm.com/index.php?rid=4802486&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544165%26dopt%3DAbstract Authors: Jitendra S, Vinay R Literature shows that Flaviviruses cause a variety of diseases, including fevers, encephalitis, and hemorrhagic fevers. NS3 is a multifunctional protein with an Nterminal protease domain (NS3pro) that is responsible for proteolytic processing of the viral polyprotein, and a C-terminal region that contains an RNA triphosphatase, RNA helicase and RNA-stimulated NTPase domain that are essential for RNA replication. Therefore, NS3 protein is the preferential choice for inhibition to stop the proteolytic processing. Hence, the 3D structure of NS3 protein was modeled using homology modeling by MODELLER 9v7. Evaluation of the constructed NS3 protein models were done by PROCHECK, VERYFY3D and through ProSA calculations. Ligands for the catalytic triad were designed... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802486 Tue, 10 May 2011 06:45:03 +0100 4802486 http://www.medworm.com/index.php?rid=4802485&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544166%26dopt%3DAbstract Authors: Kumar V A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the -1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802485 Tue, 10 May 2011 06:45:03 +0100 4802485 http://www.medworm.com/index.php?rid=4802484&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544167%26dopt%3DAbstract Authors: Prasad PK, Goswami LM, Tandon V, Chatterjee A Food-borne fluke infections/trematodiases are emerging as a major public health problem worldwide with over 40 million people affected and over 10% of world population at risk of infection. The major concentration of these infections is in Southeast Asian and Western Pacific Regions, where the epidemiological factors (including the prevalent socio-cultural food habits) are conducive for transmission of these infections. The preponderance of these infections is usually in food deficit poor communities that lack access to proper sanitary infrastructure. While targeting health for all, especially the poor rural tribal communities, it is imperative to take these infections into account. Bayesian analysis phylogeny of food-borne tremato... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802484 Tue, 10 May 2011 06:45:03 +0100 4802484 http://www.medworm.com/index.php?rid=4802483&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544168%26dopt%3DAbstract Authors: Chhabra G, Dixit A, C Garg L The alpha subunit of Mycobacterial DNA polymerase III holo enzyme catalyzes the polymerization of both DNA strands. The present investigation reports three dimensional (3-D) structure model of DNA polymerase III α subunit of Mycobacterium tuberculosis H37Rv (MtbDnaE1) generated using homology modeling with the backbone structure of DNA polymerase III α of Thermus aquaticus as a template. The model was evaluated at various structure verification servers, which assess the stereo chemical parameters of the residues in the model, as well as structural and functional domains. Comparative analysis of MtbDnaE1 structure reveals the structure of its catalytic domain to be unrelated to that of the human. Successful docking of known inhibitor of bacterial ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802483 Tue, 10 May 2011 06:45:03 +0100 4802483 http://www.medworm.com/index.php?rid=4802482&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544169%26dopt%3DAbstract Authors: Adinarayana KP, Devi RK The dihydrofolate reductase (DHFR) domain of P. falciparum is one of the few well defined targets in malarial chemotherapy. The enzyme catalyzes the nicotinamide adenine dinucleotide phosphate (NADPH) dependent reduction of dihydrofolate to tetrahydrofolate. Protein-ligand interactions were studied using DHFR protein 2BL9, extracted from PDB to evaluate the strength of affinity of various molecules towards ligand binding site and to study the extent of correlation between experimental values and computational dock scores. AutoDock runs resulted in binding energy scores from -7.14 to -10.72 kcal/mol. Among the five inhibitors (Bioorganic and Medicinal Chemistry Letters 15 2005 531-533) selected for docking studies, an excellent correlation was observed i... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802482 Tue, 10 May 2011 06:45:03 +0100 4802482 http://www.medworm.com/index.php?rid=4802481&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544170%26dopt%3DAbstract Authors: Suresh PS, Olubiyi O, Thirunavukkarasu C, Strodel B, Kumar MS Alkaline sphingomyelinase, which is expressed in the human intestine and hydrolyses sphingomyelin, is a component of the plasma and the lysosomal membranes. Hydrolase of sphingomyelin generates ceramide, sphingosine, and sphingosine 1-phosphate that have regulatory effects on vital cellular functions such as proliferation, differentiation, and apoptosis. The enzyme belongs to the Nucleotide Pyrophosphatase/Phosphodiesterase family and it differs in structural similarity with acidic and neutral sphingomyelinase. In the present study we modeled alkaline sphingomyelinase using homology modeling based on the structure of Nucleotide Pyrophosphatase/Phosphodiesterase from Xanthomonas axonopodis with which it shares 34% id... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802481 Tue, 10 May 2011 06:45:03 +0100 4802481 http://www.medworm.com/index.php?rid=4802480&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544171%26dopt%3DAbstract Authors: Do LH, Bier E Redundancy among sequence identifiers is a recurring problem in bioinformatics. Here, we present a rapid and efficient method of fingerprinting identifiers to ascertain whether two or more aliases are identical. A number of tools and approaches have been developed to resolve differing names for the same genes and proteins, however, these methods each have their own limitations associated with their various goals. We have taken a different approach to the aliasing problem by simplifying the way aliases are stored and curated with the objective of simultaneously achieving speed and flexibility. Our approach (Booly-hashing) is to link identifiers with their corresponding hash keys derived from unique fingerprints such as gene or protein sequences. This tool has prov... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802480 Tue, 10 May 2011 06:45:03 +0100 4802480 http://www.medworm.com/index.php?rid=4802479&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544172%26dopt%3DAbstract Authors: Takai-Igarashi T, Akasaka R, Suzuki K, Furukawa T, Yoshida M, Inoue K, Maruyama T, Maejima T, Bando M, Takasaki M, Sakota M, Eguchi M, Konagaya A, Matsuura H, Suzumura T, Tanaka H Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check a... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802479 Tue, 10 May 2011 06:45:03 +0100 4802479 http://www.medworm.com/index.php?rid=4802478&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21544173%26dopt%3DAbstract Authors: Ghosh TS, Mohammed MH, Komanduri D, Mande SS Given the absence of universal marker genes in the viral kingdom, researchers typically use BLAST (with stringent E-values) for taxonomic classification of viral metagenomic sequences. Since majority of metagenomic sequences originate from hitherto unknown viral groups, using stringent e-values results in most sequences remaining unclassified. Furthermore, using less stringent e-values results in a high number of incorrect taxonomic assignments. The SOrt-ITEMS algorithm provides an approach to address the above issues. Based on alignment parameters, SOrt-ITEMS follows an elaborate work-flow for assigning reads originating from hitherto unknown archaeal/bacterial genomes. In SOrt-ITEMS, alignment parameter thresholds were generated b... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4802478 Tue, 10 May 2011 06:45:03 +0100 4802478 http://www.medworm.com/index.php?rid=4696377&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464837%26dopt%3DAbstract Authors: Shamini G, Ravichandran M, Sinnott JT, Somboonwit C, Sidhu HS, Shapshak P, Kangueane P Cholera is a global disease that has persisted for millennia. The cholera toxin (CT) from Vibrio cholerae is responsible for the clinical symptoms of cholera. This toxin is a hetero-hexamer (AB(5)) complex consisting of a subunit A (CTA) with a pentamer (B(5)) of subunit B (CTB). The importance of the AB(5) complex for pathogenesis is established for the wild type O1 serogroup using known structural and functional data. However, its role is not yet documented in other known serogroups harboring sequence level residue mutations. The sequences for the toxin from different serogroups are available in GenBank (release 177). Sequence analysis reveals mutations at several sequence positions in the... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696377 Mon, 11 Apr 2011 12:45:16 +0100 4696377 http://www.medworm.com/index.php?rid=4696376&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464838%26dopt%3DAbstract Authors: Kuo HC, Ong PL, Lin JC, Huang JP Discovering amino acid (AA) patterns on protein binding sites has recently become popular. We propose a method to discover the association relationship among AAs on binding sites. Such knowledge of binding sites is very helpful in predicting protein-protein interactions. In this paper, we focus on protein complexes which have protein-protein recognition. The association rule mining technique is used to discover geographically adjacent amino acids on a binding site of a protein complex. When mining, instead of treating all AAs of binding sites as a transaction, we geographically partition AAs of binding sites in a protein complex. AAs in a partition are treated as a transaction. For the partition process, AAs on a binding site are projected from... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696376 Mon, 11 Apr 2011 12:45:16 +0100 4696376 http://www.medworm.com/index.php?rid=4696375&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464839%26dopt%3DAbstract Authors: Sharma A, Chaudhary PP, Sirohi SK, Saxena J The F420-dependent NADP oxidoreductase enzyme from Methanobrevibacter smithii catalyzes the important electron transfer step during methanogenesis. Therefore, it may act as potential target for blocking the process of methane formation. Its protein sequence is available in GenBank (accession number: ABQ86254.1) however no report has been found about its 3D protein structure. In this work, we first time claim 3D model structure of F420-dependent NADP oxidoreductase enzyme from Methanobrevibacter smithii by comparative homology modeling method. Swiss model and ESyPred3d (via Modeller 6v2) software's were generated the 3D model by detecting 1JAX (A) as template along with sequence identities of 34.272% and 35.40%. Furthermore, PROCHECK ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696375 Mon, 11 Apr 2011 12:45:16 +0100 4696375 http://www.medworm.com/index.php?rid=4696374&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464840%26dopt%3DAbstract Authors: Dikhit MR, Nathasharma YP, Patel L, Rana SP, Sahoo GC, Das P A complete understanding of different protein functional families and template information opens new avenues for novel drug development. Protein identification and analysis software performs a central role in the investigation of proteins and leads to the development of refined database for description of proteins of different Leishmania strains. There are certain databases for different strains that lack template information and functional family annotation. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has developed a web-based unique database to provide information about functional families of different proteins and its template information in different Leishmania species. Based on the template... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696374 Mon, 11 Apr 2011 12:45:16 +0100 4696374 http://www.medworm.com/index.php?rid=4696373&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464841%26dopt%3DAbstract This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns. PMID: 21464841 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696373 Mon, 11 Apr 2011 12:45:16 +0100 4696373 http://www.medworm.com/index.php?rid=4696372&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464842%26dopt%3DAbstract Authors: Singh S, Singh G, Singh AK, Gautam G, Farmer R, Lodhi SS, Wadhwa G Trichomonas vaginalis causes trichomoniasis, second most sexually transmitted disease. The genome sequence draft of T. vaginalis was published by The Institute of Genomic Research reveals an abnormally large genome size of 160 Mb. It was speculated that a significant portion of the proteome contains paralogous proteins. The present study was aimed at identification and analysis of the paralogous proteins. The all against all search approach is used to identify the paralogous proteins. The dataset of proteins was retrieved from TIGR and TrichDB FTP server. The BLAST-P program performed all against all database searches against the protein database of Trichomonas vaginalis available at NCBI genome database. In th... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696372 Mon, 11 Apr 2011 12:45:16 +0100 4696372 http://www.medworm.com/index.php?rid=4696371&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464843%26dopt%3DAbstract Authors: Cherian S, Hil P, Mishra AC To understand the reported cross-reactivity of the 2009 H1N1 and the 1918 H1N1 pandemic viruses we docked the crystal structure of 2D1, an antibody derived from a survivor of the 1918 pandemic, to the structures of hemaglutinin (HA) of the 2009 strain and seasonal H1 vaccine strains. Our studies revealed that 2D1 binds to the 2009 HA at antigenic site 'Sa', with stabilizing contacts, similar to that in an available co-crystal structure of 2D1-1918 HA. However, 2D1 failed to bind to the known antigenic sites in the HAs of seasonal strains. Our study thus reveals the molecular basis for pre-existing immunity in elderly people to the 2009 pandemic virus. PMID: 21464843 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696371 Mon, 11 Apr 2011 12:45:16 +0100 4696371 http://www.medworm.com/index.php?rid=4696370&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464844%26dopt%3DAbstract Authors: Barkhordarian A, Iyer N, Shapshak P, Somboonwit C, Sinnott J, Chiappelli F Influenza A virus is a serious public health threat. Most recently the 2009/H1N1 pandemic virus had an inherent ability to evade the host's immune surveillance through genetic drift, shift, and genomic reassortment. Immune characterization of 2009/H1N1 utilized monoclonal antibodies, neutralizing sera, and proteomics. Increased age may have provided some degree of immunity, but vaccines against seasonal influenza viruses seldom yield cross-reactive immunity, exemplified by 2009/H1N1. Nonetheless, about 33% of individuals, over the age of 60, had cross-reactive neutralizing antibodies against 2009/H1N1, whereas only 6-9% young adults had these antibodies. Children characteristically had no detectable imm... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696370 Mon, 11 Apr 2011 12:45:16 +0100 4696370 http://www.medworm.com/index.php?rid=4696369&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464845%26dopt%3DAbstract Authors: Chandra V, Ramakrishnan R, Ramanathan S Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occurs approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs), lead to amino acid changes in the protein product may account for nearly half of the known genetic variations linked to inherited human diseases and cancer. One of the main problems of medical genetics today is to identify nsSNPs that underlie disease-related phenotypes in humans. An attempt was made to develop a new approach to predict such nsSNPs. This would enhance our understanding of genetic diseases and helps to predict the disease. We detect nsSNPs and all possible and reliable alleles by ANN, a soft computing model using potential SNP in... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696369 Mon, 11 Apr 2011 12:45:16 +0100 4696369 http://www.medworm.com/index.php?rid=4696368&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21464846%26dopt%3DAbstract Authors: Ndukum J, Atlas M, Datta S In recent years, mass spectrometry has become one of the core technologies for high throughput proteomic profiling in biomedical research. However, reproducibility of the results using this technology was in question. It has been realized that sophisticated automatic signal processing algorithms using advanced statistical procedures are needed to analyze high resolution and high dimensional proteomic data, e.g., Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) data. In this paper we present a software package-pkDACLASS based on R which provides a complete data analysis solution for users of MALDITOF raw data. Complete data analysis comprises data preprocessing, monoisotopic peak detection through statistical model fitting and te... Bioinformation journals http://www.medworm.com/rss/comments.php?id=4696368 Mon, 11 Apr 2011 12:45:16 +0100 4696368