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Estimating sufficient statistics in co-evolutionary analysis by mutual information.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present results on such effects in finite-sized biological data sets and point to future research directions. We are most of all concerned with bacterial, ribosomal proteins as a prototypical example in molecular evolution. We compare to previous published suggestions, give an empirical formula, and propose a protocol to guide future research projects. PMID: 19910254 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 23, 2009 Category: Bioinformatics Authors: Weil P, Hoffgaard F, Hamacher K Tags: Comput Biol Chem Source Type: journals

Promoters of the genes encoding the transcription factors regulating the cytokine gene expression in macrophages contain putative binding sites for aryl hydrocarbon receptor.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The computer system SITECON was used to study the regulatory regions in the transcription factor genes expressed in the activated macrophage and the genes of the proteins mediating the macrophage involvement in the immune response. Dioxin responsive elements (DREs), the specific sites responsible for expression regulation of the genes involved in the cell response to dioxin, were found in these gene regions. Thus, the role of dioxin in activity regulation of the genes involved in development of the immune response can be regulated both directly, by the transcription complex containing dioxin as a ligand, and indirectly...
Source: Computational Biology and Chemistry - October 23, 2009 Category: Bioinformatics Authors: Furman DP, Oshchepkova EA, Oshchepkov DY, Shamanina MY, Mordvinov VA Tags: Comput Biol Chem Source Type: journals

Predicting melting temperature directly from protein sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We examined 75 complete microbial genomes using the Tm Index, and the analysis clearly differentiated hyperthermophilic from mesophilic microorganisms on this global genomic basis. These results are consistent with the previous hypothesis that hyperthermophiles express a greater number of high Tm proteins compared with mesophiles. The Tm Index will be valuable for modifying existing proteins (enzymes, protein drugs and vaccines) or designing novel proteins having a desired melting temperature. PMID: 19896904 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 20, 2009 Category: Bioinformatics Authors: Ku T, Lu P, Chan C, Wang T, Lai S, Lyu P, Hsiao N Tags: Comput Biol Chem Source Type: journals

Computer-assisted identification of small-molecule Bcl-2 modulators.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Apoptosis, the programmed cell death, is a highly regulated process, necessary for normal development and homeostasis of the functions of organisms. The Bcl-2 inhibitors BH3I-1 and BH3I-2 were used as lead compounds to find possible Bcl-2 or Bcl-X(L) inhibitors by using computer-assisted screening with our in-house database, containing more than four million commercially available molecules. Identified compounds were further investigated regarding their possible application as a drug. PMID: 19889579 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 12, 2009 Category: Bioinformatics Authors: Füllbeck M, Gebhardt N, Hossbach J, Daniel PT, Preissner R Tags: Comput Biol Chem Source Type: journals

On selecting mRNA isoform features for profiling prostate cancer.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Alternative splicing of human pre-mRNA is a very common phenomenon and is a major contributor to proteome diversity. mRNA isoforms that arise as a result of alternative splicing also provide a more complete picture of the transcriptome as they reflect the additional processing a pre-mRNA undergoes before being translated into a functional product. It has been reported that molecular alterations of cells can occur as a result of the differential expression of mRNA isoforms, resulting in cancerous or normal tissue. Quantification of mRNA isoforms can thus be used as a better indicator in distinguishing a normal tissue fr...
Source: Computational Biology and Chemistry - October 9, 2009 Category: Bioinformatics Authors: Nair TM Tags: Comput Biol Chem Source Type: journals

Profiling of molecular pathways regulated by microRNA 601.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we examined the effect of hsa-miR-601 on gene expression changes in human lung cancer cells A549. To achieve this, DNA microarray and global pathway analyses were performed on hsa-miR-601 introduced cells for two successive days. Gene ontology analysis revealed that the effect of hsa-miR-601 over-represented the negative regulation of translation/translational initiation, whereas GenMAPP analysis revealed that several characteristic pathways were changed in hsa-miR-601 introduced A549 cells compared to control short RNA introduced cells. Among them, up-regulation of actin cytoskeleton and down-regulation of ...
Source: Computational Biology and Chemistry - October 2, 2009 Category: Bioinformatics Authors: Ohdaira H, Nakagawa H, Yoshida K Tags: Comput Biol Chem Source Type: journals

Modelling effects of geoengineering options in response to climate change and global warming: Implications for coral reefs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Climate change will have serious effects on the planet and on its ecosystems. Currently, mitigation efforts are proving ineffectual in reducing anthropogenic CO(2) emissions. Coral reefs are the most sensitive ecosystems on the planet to climate change, and here we review modelling a number of geoengineering options, and their potential influence on coral reefs. There are two categories of geoengineering, shortwave solar radiation management and longwave carbon dioxide removal. The first set of techniques only reduce some, but not all, effects of climate change, while possibly creating other problems. They also do not ...
Source: Computational Biology and Chemistry - October 2, 2009 Category: Bioinformatics Authors: Crabbe MJ Tags: Comput Biol Chem Source Type: journals

On "A comment on 'Prediction of protein structural classes by a new measure of information discrepancy"'Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This note points out that the comment article by Kedarisetti et al. (2006a, refer to 'K-comment' hereafter) was based on the code analysis with methodological and mathematical errors. The incorrect modification of the original code and FDOD method has resulted in the wrong conclusions in K-comment. PMID: 19815464 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - September 15, 2009 Category: Bioinformatics Authors: Jin L, Fang W Tags: Comput Biol Chem Source Type: journals

Computational analysis and in vivo validation of a microRNA encoded by the IBTK gene, a regulator of B-lymphocytes differentiation and survival.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are small single-stranded RNA molecules that play an essential role in the regulation of gene expression and cell physiology. Gene rearrangements occurring in the miRNA sequence are associated with cancer. The IBTK genetic locus is located in the genomic sequence 6q14.1 that undergoes chromosomal aberration in lymphoproliferative disorders. The IBTK gene encodes the proteins IBtk-alpha, beta and gamma that regulate the B cell receptor signalling through Bruton's tyrosine kinase, which promotes B cell survival and differentiation. Pro-MirII-based analysis predicted four precursors of microRNAs (pre-mi...
Source: Computational Biology and Chemistry - September 5, 2009 Category: Bioinformatics Authors: Fiume G, Rossi A, Di Salle E, Spatuzza C, Mallardo M, Scala G, Quinto I Tags: Comput Biol Chem Source Type: journals

Classification for high-throughput data with an optimal subset of principal components.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
High-throughput data have been widely used in biological and medical studies to discover gene and protein functions. Due to the high dimensionality, principal component analysis (PCA) is often involved for data dimension reduction. However, when a few principal components (PCs) are selected for dimension reduction or considered for dimension determination, they are typically ranked by their variances, eigenvalues. However, this approach is not always effective in subsequent multivariate analysis, particularly classification. To maximize information from data with a subset of the components, we apply a different ranking...
Source: Computational Biology and Chemistry - August 17, 2009 Category: Bioinformatics Authors: Song JJ, Ren Y, Yan F Tags: Comput Biol Chem Source Type: journals

Algebraic methods for inferring biochemical networks: A maximum likelihood approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current method, unlike some of the graphical approaches proposed in the literature, uses the values of the experimental measurements only relative to the geometry of the biochemical reactions under the assumption that the underlying reaction network is the same for all the experiments. The proposed approach utilizes algebraic statistical methods in order to parametrize the set of possible reactions...
Source: Computational Biology and Chemistry - August 5, 2009 Category: Bioinformatics Authors: Craciun G, Pantea C, Rempala GA Tags: Comput Biol Chem Source Type: journals

Editors' note concerning a development of database analysis by Smith and Stein (2009).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19700369 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - August 2, 2009 Category: Bioinformatics Authors: Crabbe MJ, Konopka AK Tags: Comput Biol Chem Source Type: journals

Two-phase biomedical named entity recognition using CRFs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
As a fundamental step of biomedical text mining, Biomedical Named Entity Recognition (Bio-NER) remains a challenging task. This paper explores a so-called two-phase approach to identify biomedical entities, in which the recognition task is divided into two subtasks: Named Entity Detection (NED) and Named Entity Classification (NEC). And the two subtasks are finished in two phases. At the first phase, we try to identify each named entity with a Conditional Random Fields (CRFs) model without identifying its type; at the second phase, another CRFs model is used to determine the correct entity type for each identified enti...
Source: Computational Biology and Chemistry - August 2, 2009 Category: Bioinformatics Authors: Li L, Zhou R, Huang D Tags: Comput Biol Chem Source Type: journals

Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The spread efficiency of influenza virus is significantly affected by several environmental parameters. However, neither the underlying reasons, nor the exact character and magnitude of the phenomena involved are sufficiently well understood. Here we present a probabilistic approach to the virus transmission events. For a sample ensemble, we construct a model of the infectivity as a function of the ambient conditions, and we determine its parameter values on the basis of the available experimental data. PMID: 19656728 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - August 2, 2009 Category: Bioinformatics Authors: Zuk T, Rakowski F, Radomski JP Tags: Comput Biol Chem Source Type: journals

Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular dockin...
Source: Computational Biology and Chemistry - July 22, 2009 Category: Bioinformatics Authors: Lauria A, Ippolito M, Almerico AM Tags: Comput Biol Chem Source Type: journals

A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We develop a multi-level model, using ordinary differential equations, based on quantitative experimental data, accounting for murine erythropoiesis. At the sub-cellular level, the model includes a description of the regulation of red blood cell differentiation through Epo-stimulated JAK2-STAT5 signalling activation, while at the cell population level the model describes the dynamics of (STAT5-mediated) red blood cell differentiation from their progenitors. Furthermore, the model includes equations depicting the hypoxia-mediated regulation of hormone erythropoietin blood levels. Take all together, the model constitutes...
Source: Computational Biology and Chemistry - July 8, 2009 Category: Bioinformatics Authors: Lai X, Nikolov S, Wolkenhauer O, Vera J Tags: Comput Biol Chem Source Type: journals

Exploiting three kinds of interface propensities to identify protein binding sites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we present a building block of proteins called order profiles to use the evolutionary information of the protein sequence frequency profiles and apply this building block to produce a class of propensities called order profile interface propensities. For comparisons, we revisit the usage of residue interface propensities and binary profile interface propensities for protein binding site prediction. Each kind of propensities combined with sequence profiles and accessible surface areas are inputted into SVM. When tested on four types of complexes (hetero-permanent complexes, hetero-transient complexes, homo-pe...
Source: Computational Biology and Chemistry - July 8, 2009 Category: Bioinformatics Authors: Liu B, Wang X, Lin L, Dong Q, Wang X Tags: Comput Biol Chem Source Type: journals

Upstream curved sequences in E. coli are related to the regulation of transcription initiation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The advancement in Escherichia coli genome research has made the information regarding transcription start sites of many genes available. A study relying on the availability of transcription start locations was performed. The first question addressed was what an average DNA curvature profile upstream of genes would look like when these genes are aligned by transcription start sites in comparison to alignment by translation start sites. Since it was hypothesized that curvature plays a role in transcription regulation, the expectation was that curvature measurements relative to transcription starts, rather than translati...
Source: Computational Biology and Chemistry - July 6, 2009 Category: Bioinformatics Authors: Nov Klaiman T, Hosid S, Bolshoy A Tags: Comput Biol Chem Source Type: journals

Population-based local search for protein folding simulation in the MJ energy model and cubic lattices.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the populati...
Source: Computational Biology and Chemistry - July 2, 2009 Category: Bioinformatics Authors: Kapsokalivas L, Gan X, Albrecht AA, Steinhöfel K Tags: Comput Biol Chem Source Type: journals

Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Total GC-content (G+C), GC-content in codon positions and 0-fold, 2-fold and 4-fold degenerated sites in all coding districts from 10 completely sequenced genomes of simplex and varicello viruses have been calculated by the original "Coding Genome Scanner" algorithm. The low coefficient of correlation (R<0.5) between 3GC and G+C in all coding districts from unique regions (UL and US) of alphaherpesvirus genome is a new criterion of the strong mutational pressure that is the process of increasing the rates of nonsynonymous mutations because of the extreme saturation (GC-pressure) or desaturation (AT-pressure) of thir...
Source: Computational Biology and Chemistry - June 26, 2009 Category: Bioinformatics Authors: Khrustalev VV, Barkovsky EV Tags: Comput Biol Chem Source Type: journals

Foldable subunits of helix protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Detection of foldable subunits in proteins is an important approach to understand their evolutions and find building motifs for de novo protein design. Using united-residue model, we simulated the folding of a six-helix protein with a length of 120 amino acids (C-terminal domain of Ku86). The folding behaviors, structural topology and sequence repetition of this protein all suggest that it may have a two-fold quasi-repetition or symmetry in its sequence and structure. Therefore, we simulated the folding of its two halves (1-60 and 61-120 amino acids) and find that they can fold into native conformations independently. ...
Source: Computational Biology and Chemistry - June 24, 2009 Category: Bioinformatics Authors: He Y, Zhou R, Huang Y, Xiao Y Tags: Comput Biol Chem Source Type: journals

Directional persistence and the optimality of run-and-tumble chemotaxis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
E. coli does chemotaxis by performing a biased random walk composed of alternating periods of swimming (runs) and reorientations (tumbles). Tumbles are typically modelled as complete directional randomisations but it is known that in wild type E. coli, successive run directions are actually weakly correlated, with a mean directional difference of approximately 63 degrees . We recently presented a model of the evolution of chemotactic swimming strategies in bacteria which is able to quantitatively reproduce the emergence of this correlation. The agreement between model and experiments suggests that directional persisten...
Source: Computational Biology and Chemistry - June 24, 2009 Category: Bioinformatics Authors: Nicolau DV, Armitage JP, Maini PK Tags: Comput Biol Chem Source Type: journals

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: Cardiac arrhythmias, re-entry and the Halting problem.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the arsenal of tools that a computational modeller can bring to bare on the study of cardiac arrhythmias, the most widely used and arguably the most successful is that of an excitable medium, a special case of a reaction-diffusion model. These are used to simulate the internal chemical reactions of a cardiac cell and the diffusion of their membrane voltages. Via a number of different methodologies it has previously been shown that reaction-diffusion systems are at multiple levels Turing complete. That is, they are capable of computation in the same manner as a universal Turing machine. However, all such computationa...
Source: Computational Biology and Chemistry - June 10, 2009 Category: Bioinformatics Authors: Scarle S Tags: Comput Biol Chem Source Type: journals

Search of regular sequences in promoters from eukaryotic genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, the notion of "regularity" is introduced to describe the structural features of DNA sequences. This notion expands the "latent periodicity" term. The novel method for revealing regularity based on the runs test is described. The search of regular sequences in eukaryotic promoters has shown that more than 60% of them possess a regularity property on statistically significant level. Possible biological functions of regularity are discussed together with the possibility of using this characteristic for performing promoter annotation. PMID: 19395315 [PubMed - in process] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Shelenkov A, Korotkov E Tags: Comput Biol Chem Source Type: journals

Hybrid stochastic simulations of intracellular reaction-diffusion systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetic...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Kalantzis G Tags: Comput Biol Chem Source Type: journals

The gene network determining development of Drosophila melanogaster mechanoreceptors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Macrochaetes (large bristles), functioning as mechanoreceptors, are located in an orderly fashion on the drosophila head and body forming a species-specific bristle pattern. A simple organization of each bristle organ, comprising only four specialized cells, and conservation of bristle pattern make macrochaetes a convenient model for studying the development patterns of spatial structures with a fixed number of elements at certain positions and the mechanisms of cell differentiation. In this work, we systematize the experimental data on the main genes and their products that are involved in the control of proneural clu...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Furman DP, Bukharina TA Tags: Comput Biol Chem Source Type: journals

Supervised machine learning algorithms for protein structure classification.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We explore automation of protein structural classification using supervised machine learning methods on a set of 11,360 pairs of protein domains (up to 35% sequence identity) consisting of three secondary structure elements. Fifteen algorithms from five categories of supervised algorithms are evaluated for their ability to learn for a pair of protein domains, the deepest common structural level within the SCOP hierarchy, given a one-dimensional representation of the domain structures. This representation encapsulates evolutionary information in terms of sequence identity and structural information characterising the se...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Jain P, Garibaldi JM, Hirst JD Tags: Comput Biol Chem Source Type: journals

Ambush hypothesis revisited: Evidences for phylogenetic trends.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, but either at the second (+1 frame-shift) or the third (-1 frame-shift) nucleotide of the codon. Coding sequences lack stop codons, but frame-shifted sequences contain many stop codons, termed off-frame stops or hidden stops. These hidden stops terminate frame-shifted translation, potentially decreasing ene...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Singh TR, Pardasani KR Tags: Comput Biol Chem Source Type: journals

ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of ami...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Vishnepolsky B, Pirtskhalava M Tags: Comput Biol Chem Source Type: journals

Whole genome assembly from 454 sequencing output via modified DNA graph concept.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA assembly algorithm which deals well with such data and outperforms other assembly algorithms used in practice. The constructed SR-ASM algorithm is a heuristic method based on a graph model, the graph being a modified DNA graph proposed for DNA sequencing by hybridization proce...
Source: Computational Biology and Chemistry - June 1, 2009 Category: Bioinformatics Authors: Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L Tags: Comput Biol Chem Source Type: journals

A model of influenza virus spread as a function of temperature and humidity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of ...
Source: Computational Biology and Chemistry - March 8, 2009 Category: Bioinformatics Authors: Zuk T, Rakowski F, Radomski JP Tags: Comput Biol Chem Source Type: journals

A comparative study of the single crystal X-ray determination and molecular modelling of the binding of oligomycin to ATP Synthase.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently published X-ray structures of three common forms, A, B and C, of oligomycin, including absolute configurations, are investigated to examine their binding to ATP Synthase. The X-ray studies reveal regions with differences in three-dimensional structure and hydrogen bonding propensity between the oligomycins, which may be associated with their potential to bind to sites on ATP Synthase. Computational docking studies carried out using MOE with the X-ray structures and an homology model of the F(O) domain of ATP Synthase from Escherichia coli, are used to derive an induced fit pocket. Docking of all oligomycins to...
Source: Computational Biology and Chemistry - January 19, 2009 Category: Bioinformatics Authors: Green RC, Thumser AE, Povey D, Saldanha JW, Potter BS, Palmer RA, Howlin BJ Tags: Comput Biol Chem Source Type: journals

Design of multiplex PCR primers using heuristic algorithm for sequential deletion applications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study obtains a near-optimal solution of primer sets that can be placed in as few test tubes as possible for one multiplex PCR experiment. RESULTS: Homo sapiens ribosomal protein L5, Homo sapiens xylosyltransferase I, and Bacteriophage T4 gene product 11 were used as test examples to verify efficacy of the proposed algorithm. In addition, the designed primers of Homo sapiens ribosomal protein L5 cDNA were applied in multiplex PCR experiments. A total of 48 forward primers and one reverse primer were designed and used to duplicate N-terminal truncated mutants of different lengths from the protein. The primers were clas...
Source: Computational Biology and Chemistry - January 15, 2009 Category: Bioinformatics Authors: Chen YF, Chen RC, Chan YK, Pan RH, Hseu YC, Lin E Tags: Comput Biol Chem Source Type: journals

A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The nicotinic acetylcholine receptor (nAChR) is a member of the ligand-gated ion channel family and is implicated in many neurological events. Yet, the receptor is difficult to target without high-resolution structures. In contrast, the structure of the acetylcholine binding protein (AChBP) has been solved to high resolution, and it serves as a surrogate structure of the extra-cellular domain in nAChR. Here we conduct a virtual screening study of the AChBP using the relaxed-complex method, which involves a combination of molecular dynamics simulations (to achieve receptor structures) and ligand docking. The library scr...
Source: Computational Biology and Chemistry - January 8, 2009 Category: Bioinformatics Authors: Babakhani A, Talley TT, Taylor P, McCammon JA Tags: Comput Biol Chem Source Type: journals

Sequence assembly.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html. PMID: 19152793 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - December 6, 2008 Category: Bioinformatics Authors: Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J Tags: Comput Biol Chem Source Type: journals

A rebuttal to the comments on the genome order index.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently, Elhaik et al. [Elhaik, E., Graur, D., Josic, K., 2008. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. Comp. Biol. Chem. 32, 147] commented on the genome order index, which is defined as S=a(2)+c(2)+g(2)+t(2) where a, c, g and t denote corresponding base frequencies. They claimed that (1) "S<1/3 is in fact a mathematical property that is always true", and (2) "S is strictly equivalent to and derivable from the Shannon H function". The first claim is apparently wrong: for instance, when a=c=0.5, g=t=0, S=0.5>1/3. The second claim is also incorrect b...
Source: Computational Biology and Chemistry - November 14, 2008 Category: Bioinformatics Authors: Zhang R Tags: Comput Biol Chem Source Type: journals

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophi...
Source: Computational Biology and Chemistry - August 31, 2008 Category: Bioinformatics Authors: Maugini E, Tronelli D, Bossa F, Pascarella S Tags: Comput Biol Chem Source Type: journals

Genomic splice site prediction algorithm based on nucleotide sequence pattern for RNA viruses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Splice site prediction on an RNA virus has two potential difficulties seriously degrading the performance of most conventional splice site predictors. One is a limited number of strains available for a virus species and the other is the diversified sequence patterns around the splice sites caused by the high mutation frequency. To overcome these two difficulties, a new algorithm called Genomic Splice Site Prediction (GSSP) algorithm, was proposed for splice site prediction of RNA viruses. The key idea of the GSSP algorithm was to characterize the interdependency among the nucleotides and base positions based on the eig...
Source: Computational Biology and Chemistry - August 20, 2008 Category: Bioinformatics Authors: Tsai KN, Lin SH, Shih SR, Lai JS, Chen CM Tags: Comput Biol Chem Source Type: journals

Finding rule groups to classify high dimensional gene expression datasets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microarray data provides quantitative information about the transcription profile of cells. To analyze microarray datasets, methodology of machine learning has increasingly attracted bioinformatics researchers. Some approaches of machine learning are widely used to classify and mine biological datasets. However, many gene expression datasets are extremely high dimensionality, traditional machine learning methods cannot be applied effectively and efficiently. This paper proposes a robust algorithm to find out rule groups to classify gene expression datasets. Unlike the most classification algorithms, which select dimens...
Source: Computational Biology and Chemistry - August 14, 2008 Category: Bioinformatics Authors: An J, Chen YP Tags: Comput Biol Chem Source Type: journals

Prediction of Alzheimer's diagnosis using semi-supervised distance metric learning with label propagation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Alzheimer's disease (AD) is the most common form of dementia and leads to irreversible neurogenerative damage of the brain. However, the current diagnostic tools have poor sensitivity, especially for the early stages of AD and do not allow for diagnosis until AD has lead to irreversible brain damage. Therefore, it is crucial that AD is detected as early as possible. Although it is very hard, laborious and time-consuming to gather many AD and non-AD labeled samples, gathering unlabeled samples is easier than labeled samples. Since standard learning algorithms learn a diagnosis model from labeled samples only, they requi...
Source: Computational Biology and Chemistry - August 8, 2008 Category: Bioinformatics Authors: Teramoto R Tags: Comput Biol Chem Source Type: journals

Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SNP combinations with genotypes called "SNP barcode". DBPSO are applied to generate SNP barcode, which computes the maximal difference of occurrence between the case and control groups, to predict disease susceptibility such as osteoporosis. Different SNP barcode patterns may occur several times in either lo...
Source: Computational Biology and Chemistry - August 8, 2008 Category: Bioinformatics Authors: Chang HW, Yang CH, Ho CH, Wen CH, Chuang LY Tags: Comput Biol Chem Source Type: journals

PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The automatic assignment of secondary structure from three-dimensional atomic coordinates of proteins is an essential step for the analysis and modeling of protein structures. So different methods based on different criteria have been designed to perform this task. We introduce a new method for protein secondary structure assignment based solely on C(alpha) coordinates. We introduce four certain relations between C(alpha) three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: alpha-helix, 3(10)-helix, pi-helix and beta-strand. In our appro...
Source: Computational Biology and Chemistry - August 6, 2008 Category: Bioinformatics Authors: Hosseini SR, Sadeghi M, Pezeshk H, Eslahchi C, Habibi M Tags: Comput Biol Chem Source Type: journals

A simple method of identifying symmetric substructures of proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Accurate identifications of internal symmetric substructures of proteins are needed in protein evolution study and protein design. To overcome the difficulties met by previous methods, here we propose a simple quantitative one by using a similarity matrix plus Pearson's correlation analysis. The distance root-mean-square deviation (dRMSD) is used to measure the similarity of two substructures in a protein. We applied this method to the proteins of the beta-propeller, jelly roll, and beta-trefoil families and the results show that this method cannot only detect the internal repetitive structures in proteins effectively,...
Source: Computational Biology and Chemistry - August 3, 2008 Category: Bioinformatics Authors: Chen H, Huang Y, Xiao Y Tags: Comput Biol Chem Source Type: journals

Computational identification of novel microRNA homologs in the chimpanzee genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed the chimp homologs of the human pre-miRNA and mature miRNA sequences. Based on a homology search of the chimpanzee genome with human miRNA precursor sequences as queries, we identified 639 chimp miRNA genes, including 529 novel chimp miRNAs. 91.8% of chimp mature miRNAs and 60.3% of precursors are 100% identical to their human orthologs. The pre-miRNA secondary structures, miRNA families, and clusters are also highly conserved. We also found certain sequence differences in pre-miRNAs and even mature miRNAs...
Source: Computational Biology and Chemistry - July 26, 2008 Category: Bioinformatics Authors: Baev V, Daskalova E, Minkov I Tags: Comput Biol Chem Source Type: journals

A fundamental study of the PCR amplification of GC-rich DNA templates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A theoretical analysis is presented with experimental confirmation to conclusively demonstrate the critical role that annealing plays in efficient PCR amplification of GC-rich templates. The analysis is focused on the annealing of primers at alternative binding sites (competitive annealing) and the main result is a quantitative expression of the efficiency (eta) of annealing as a function of temperature (T(A)), annealing period (t(A)), and template composition. The optimal efficiency lies in a narrow region of T(A) and t(A) for GC-rich templates and a much broader region for normal GC templates. To confirm the theoreti...
Source: Computational Biology and Chemistry - July 25, 2008 Category: Bioinformatics Authors: Mamedov TG, Pienaar E, Whitney SE, Termaat JR, Carvill G, Goliath R, Subramanian A, Viljoen HJ Tags: Comput Biol Chem Source Type: journals

Aggregation mechanism investigation of the GIFQINS cross-beta amyloid fibril.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we intend to utilize room temperature simulation to study the stability of the modeling structure for GIFQINS. The results suggest that the hexamer of GIFQINS is highly stable and consistent with the prediction of Eisenberg. Furthermore, high-temperature molecular dynamics simulation in explicit water is used to study its aggregation mechanisms. The important findings from this work are (a) dimer is not thermodynamically stable state, (b) dissolution of the fibrils is more difficult than aggregation, (c) tetramer (2-2) is the intermediate state and (d) two transition states are corresponding to trimer (2-1) ...
Source: Computational Biology and Chemistry - July 25, 2008 Category: Bioinformatics Authors: Chen HF Tags: Comput Biol Chem Source Type: journals

A feature vector integration approach for a generalized support vector machine pairwise homology algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Due to the exponential growth of sequenced genomes, the need to quickly provide accurate annotation for existing and new sequences is paramount to facilitate biological research. Current sequence comparison approaches fail to detect homologous relationships when sequence similarity is low. Support vector machine (SVM) algorithms approach this problem by transforming all proteins into a feature space of equal dimension based on protein properties, such as sequence similarity scores against a basis set of proteins or motifs. This multivariate representation of the protein space is then used to build a classifier specific...
Source: Computational Biology and Chemistry - July 16, 2008 Category: Bioinformatics Authors: Webb-Robertson BJ, Oehmen CS, Shah AR Tags: Comput Biol Chem Source Type: journals

Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene expression data sets hold the promise to provide cancer diagnosis on the molecular level. However, using all the gene profiles for diagnosis may be suboptimal. Detection of the molecular signatures not only reduces the number of genes needed for discrimination purposes, but may elucidate the roles they play in the biological processes. Therefore, a central part of diagnosis is to detect a small set of tumor biomarkers which can be used for accurate multiclass cancer classification. This task calls for effective multiclass classifiers with built-in biomarker selection mechanism. We propose the sparse optimal scorin...
Source: Computational Biology and Chemistry - July 16, 2008 Category: Bioinformatics Authors: Leng C Tags: Comput Biol Chem Source Type: journals

Identifying the target mRNAs of microRNAs in colorectal cancer.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) play an important role in gene regulatory networks by inhibiting the expression of target mRNAs. There is a growing interest in identifying the relationship between miRNAs and their target mRNAs. Various experimental studies have been carried out to discover miRNAs involved in cancer and to identify their target genes. At the same time, a large volume of miRNA and mRNA expression profiles have become available owing to the development of high-throughput measurement technologies. So, there is now a pressing need to develop a computational method by which we can identify the target mRNAs of given miRNA...
Source: Computational Biology and Chemistry - July 16, 2008 Category: Bioinformatics Authors: Kim S, Choi M, Cho KH Tags: Comput Biol Chem Source Type: journals

Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Optimally weighted fuzzy k-nearest neighbors (OWFKNN) algorithm has been used to predict proteins' subcellular locations based on their amino acid composition, in this paper. The datasets used consists of two species which are 997 prokaryotic and 2427 eukaryotic protein sequences. The overall prediction accuracy achieved is about 88.5% for prokaryotic sequences and 86.2% for eukaryotic sequences in a jackknife test. Compared to other algorithms developed for the prediction of protein subcellular location, OWFKNN gives very satisfying results. Therefore, OWFKNN can be used as an alternative method to predict protein loc...
Source: Computational Biology and Chemistry - July 16, 2008 Category: Bioinformatics Authors: Nasibov E, Kandemir-Cavas C Tags: Comput Biol Chem Source Type: journals