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 'Springer protocols feed by Bioinformatics' source. Mon, 11 Jan 2010 16:40:24 +0100 http://www.medworm.com/index.php?rid=3114768&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_9 Proteomics has advanced in leaps and bounds over the past couple of decades. However, the continuing dependency of mass spectrometry-based protein identification on the searching of spectra against protein sequence databases limits many proteomics experiments. If there is no sequenced genome for a given species, then cross species proteomics is required, attempting to identify proteins across the species boundary, typically using the sequenced genome of a closely related species. Unlike sequence searching for homologues, the proteomics equivalent is confounded by small differences in amino acid sequences, leading to large differences in peptide masses; this renders mass matching of peptides and their product ions difficult. Therefore, the phylogenetic distance between the two species and t... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114768 Thu, 12 Nov 2009 00:00:00 +0100 3114768 http://www.medworm.com/index.php?rid=3114767&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_8 The review describes methods of de novo sequencing of peptides by mass spectrometry. De novo methods utilize computational approaches to deduce the sequence or partial sequence of peptides directly from the experimental MS/MS spectra. The concepts behind a number of de novo sequencing methods are discussed. The other approach to identify peptides by tandem mass spectrometry is to match the fragment ions with virtual peptide ions generated from a genomic or protein database. De novo methods are essential to identify proteins when the genomes are not known but they are also extremely useful even when the genomes are known since they are not affected by errors in a search database. Another advantage of de novo methods is that the partial sequence can be used to search for posttranslation modi... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114767 Thu, 12 Nov 2009 00:00:00 +0100 3114767 http://www.medworm.com/index.php?rid=3114766&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_7 This article provides a concise roadmap for the proteomics researchers to start using spectral library searching in their data analysis workflow. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114766 Thu, 12 Nov 2009 00:00:00 +0100 3114766 http://www.medworm.com/index.php?rid=3114765&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_6 Tandem mass spectrometry is a widely used tool in proteomics. This section will address the properties that describe how protonated peptides fragment when activated by collisions in a mass spectrometer and how that information can be used to identify proteins. A review of the mobile proton model is presented, along with a summary of commonly observed peptide cleavage enhancements, including the proline effect. The methods used to elucidate peptide dissociation chemistry by using both small groups of model peptides and large datasets are also discussed. Finally, the role of peak intensity in commercially available and developmental peptide identification algorithms is examined. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114765 Thu, 12 Nov 2009 00:00:00 +0100 3114765 http://www.medworm.com/index.php?rid=3114764&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_5 Accurate and precise methods for estimating incorrect peptide and protein identifications are crucial for effective large-scale proteome analyses by tandem mass spectrometry. The target-decoy search strategy has emerged as a simple, effective tool for generating such estimations. This strategy is based on the premise that obvious, necessarily incorrect “decoy” sequences added to the search space will correspond with incorrect search results that might otherwise be deemed to be correct. With this knowledge, it is possible not only to estimate how many incorrect results are in a final data set but also to use decoy hits to guide the design of filtering criteria that sensitively partition a data set into correct and incorrect identifications. (Source: Springer protocols feed by Bi... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114764 Thu, 12 Nov 2009 00:00:00 +0100 3114764 http://www.medworm.com/index.php?rid=3114763&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_4 A variety of methods are described in the literature to assign peptide sequences to observed tandem MS data. Typically, the identified peptides are associated only with an arbitrary score that reflects the quality of the peptide-spectrum match but not with a statistically meaningful significance measure. In this chapter, we discuss why statistical significance measures can simplify and unify the interpretation of MS-based proteomic experiments. In addition, we also present available software solutions that convert scores into sound statistical measures. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114763 Thu, 12 Nov 2009 00:00:00 +0100 3114763 http://www.medworm.com/index.php?rid=3114762&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_3 The peptide identification problem lies at the heart of modern proteomic methodology, from which the presence of a particular protein or proteins in a sample may be inferred. The challenge is to find the most likely amino acid sequence, which corresponds to each tandem mass spectrum that has been collected, and produce some kind of score and associated statistical measure that the putative identification is correct. This approach assumes that the peptide (and parent protein) sequence in question is known and is present in the database which is to be searched, as opposed to de novo methods, which seek to identify the peptide ab initio. This chapter will provide an overview of the methods that common, popular software tools employ to search protein sequence databases to provide the non-exper... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114762 Thu, 12 Nov 2009 00:00:00 +0100 3114762 http://www.medworm.com/index.php?rid=3114761&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_2 Protein identification by mass spectrometry (MS) is an important technique in proteomics. By searching an MS spectrum against a given protein database, the most matched proteins are sorted using a scoring function and the top one is often considered the correctly identified protein. Peptide mass fingerprinting (PMF) is one of the major methods for protein identification using MS technology. It is faster and cheaper than the other popular technique - Tandem Mass Spectrometry. Key bioinformatics issues in PMF analysis include designing a scoring function to quantitatively measure the degree of consistency between a PMF spectrum and a protein sequence and assessing the confidence of identified proteins. In this chapter, we will introduce several scoring functions that were developed by others... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114761 Thu, 12 Nov 2009 00:00:00 +0100 3114761 http://www.medworm.com/index.php?rid=3114760&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_25 Proteomics attempts to characterise the gene products expressed in a cell or tissue via a range of biophysical techniques including crystallography and NMR and, more relevantly to this volume, chromatography and mass spectrometry. It is becoming increasingly clear that the native states of segments of many of the cellular proteins are not stable, folded structures, and much of the proteome is in an unfolded, disordered state. These proteins and their disordered segments have functionally interesting properties and provide novel challenges for the biophysical techniques that are used to study them. This chapter focuses on computational approaches to predicting such regions and analyzing the functions linked to them, and has implications for protein scientists who wish to study such properti... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114760 Thu, 12 Nov 2009 00:00:00 +0100 3114760 http://www.medworm.com/index.php?rid=3114759&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_24 In Proteomics, fast enhancements with regard to technology are responsible for the creation of huge data sets. Consequently, in 2006 the European Commission funded a Coordination Action named ProDaC (Proteomics Data Collection) within the 6th EU Framework Programme to foster a community-wide data collection and data sharing. The aims of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114759 Thu, 12 Nov 2009 00:00:00 +0100 3114759 http://www.medworm.com/index.php?rid=3114758&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_23 Data management and sharing in omics science is highly challenging due to the constant evolution of experimental techniques, the range of instrument types and software used for analysis, and the high volumes of data produced. The Functional Genomics Experiment (FuGE) Model was created to provide a model for capturing descriptions of sample processing, experimental protocols and multidimensional data for any kind of omics experiment. FuGE has two modes of action: (a) as a storage architecture for experimental workflows and (b) as a framework for building new technology-specific data standards. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114758 Thu, 12 Nov 2009 00:00:00 +0100 3114758 http://www.medworm.com/index.php?rid=3114757&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_22 Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provide... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114757 Thu, 12 Nov 2009 00:00:00 +0100 3114757 http://www.medworm.com/index.php?rid=3114756&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_21 Molecular interactions are crucial components of the cellular process. In order to understand this complex machinery, one needs to gather published data from various sources. Many projects have initiated the collection of interaction data for this purpose since 2002. However, the lack of standardisation previously made the task of aggregating datasets difficult. This issue has been resolved by the creation of Molecular Interaction standard in 2004 by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO). Furthermore, major database providers have come together with the goal to exchange data in order to optimise laborious curation tasks. Finally, tools and frameworks have been created based on PSI-MI standards to facilitate the visualis... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114756 Thu, 12 Nov 2009 00:00:00 +0100 3114756 http://www.medworm.com/index.php?rid=3114755&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_20 The PRIDE Proteomics Identifications Database provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues and disease states. A PRIDE experiment typically includes identifications of proteins, peptides and protein modifications. Many of the submitted experiments also include processed peak lists representing the mass spectra that provide the evidence for these identifications. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114755 Thu, 12 Nov 2009 00:00:00 +0100 3114755 http://www.medworm.com/index.php?rid=3114754&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_1 This book is part of the Methods in Molecular Biology series, and provides a general overview of computational approaches used in proteome research. In this chapter, we give an overview of the scope of the book in terms of current proteomics experimental techniques and the reasons why computational approaches are needed. We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114754 Thu, 12 Nov 2009 00:00:00 +0100 3114754 http://www.medworm.com/index.php?rid=3114753&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_19 PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw data is returned to the community via several web-based data exploration tools. The PeptideAtlas resource is useful for experiment planning, improving genome annotation, and other data mining projects. PeptideAtlas has become especially useful for planning targeted proteomics experiments. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114753 Thu, 12 Nov 2009 00:00:00 +0100 3114753 http://www.medworm.com/index.php?rid=3114752&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_18 Protein quantification represents an important extension to identification proteomics, enabling the comparison of protein expression across different samples or treatments. Comparative protein quantification by mass spectrometry typically employs stable isotope incorporation, but recently, comparative quantification of label-free LCn-MS proteomics data has emerged as an alternative approach. In this chapter, we provide an overview of the different approaches for extracting quantitative data from label-free LCn-MS experiments. The computational procedure for recovering the quantitative information is outlined. Examples of statistical tests used to evaluate the relevance of results are also provided. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114752 Thu, 12 Nov 2009 00:00:00 +0100 3114752 http://www.medworm.com/index.php?rid=3114751&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_17 Isotope labeling combined with LC-MS/MS provides a robust platform for quantitative proteomics. Protein quantitation based on mass spectral data falls into two categories: one determined by MS/MS scans, e.g., iTRAQ-labeling quantitation, and the other by MS scans, e.g., quantitation using SILAC, ICAT, or 18O labeling. In large-scale LC-MS proteomic experiments, tens of thousands of MS and MS/MS spectra are generated and need to be analyzed. Data noise further complicates the data analysis. In this chapter, we present two automated tools, called Multi-Q and MaXIC-Q, for MS/MS- and MS-based quantitation analysis. They are designed as generic platforms that can accommodate search results from SEQUEST and Mascot, as well as mzXML files converted from raw files produced by various mass spectrom... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114751 Thu, 12 Nov 2009 00:00:00 +0100 3114751 http://www.medworm.com/index.php?rid=3114750&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_16 Despite recent progress in “shotgun” peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS), proteome coverage and reproducibility are still limited with this approach and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates that there is a continuing need for protein separation by two-dimensional gel electrophoresis (2-DE). However, with traditional 2-DE informatics, the digitized images are reduced to symbolic data through spot detection and quantification before proteins are compared for differential expression by spot matching. Recently, a more robust and automated paradigm has emerged where gels are directly aligned in the image domain before spots are detected across the whole... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114750 Thu, 12 Nov 2009 00:00:00 +0100 3114750 http://www.medworm.com/index.php?rid=3114749&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_15 Mass spectrometry has quickly become an essential tool in molecular biology laboratories. Here, we describe the Trans-Proteomic Pipeline, a collection of software tools, to facilitate the analysis, exchange, and comparison of MS data. The pipeline is instrument-independent and supports most commonly used proteomics workflows, including quantitative applications such as ICAT, iTRAQ, and SILAC. Importantly, the pipeline uses open, standard data formats and calculates accurate estimates of sensitivity and error rates, thus allowing for meaningful data exchange. In this chapter, we will introduce the various components of the pipeline in the context of three typical proteomic use-case scenarios. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114749 Thu, 12 Nov 2009 00:00:00 +0100 3114749 http://www.medworm.com/index.php?rid=3114748&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_14 We describe the overall concepts behind the software and illustrate its use with several examples. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114748 Thu, 12 Nov 2009 00:00:00 +0100 3114748 http://www.medworm.com/index.php?rid=3114747&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_13 Multiple reaction monitoring (MRM) of peptides is a popular proteomics technique that employs tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential protein identification studies. Using this technique, the specificity of precursor to product transitions is exploited to determine the absolute quantity of multiple proteins in a single sample. Selection of suitable transitions is critical for the success of MRM experiments, but accurate theoretical prediction of fragmentation patterns and peptide signal intensity is currently not possible. A recently proposed solution to this problem is to combine knowledge of the preferred properties of transitions for MRM, taken from expert practitioners, with MS/MS evidence extracted from a ... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114747 Thu, 12 Nov 2009 00:00:00 +0100 3114747 http://www.medworm.com/index.php?rid=3114746&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_12 High-throughput, MS-based proteomics studies are generating very large volumes of biologically relevant data. Given the central role of proteomics in emerging fields such as system/synthetic biology and biomarker discovery, the amount of proteomic data is expected to grow at unprecedented rates over the next decades. At the moment, there is pressing need for high-performance computational solutions to accelerate the analysis and interpretation of this data. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114746 Thu, 12 Nov 2009 00:00:00 +0100 3114746 http://www.medworm.com/index.php?rid=3114745&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_11 Computational proteomics applications are often imagined as a pipeline, where information is processed in each stage before it flows to the next one. Independent of the type of application, the first stage invariably consists of obtaining the raw mass spectrometric data from the spectrometer and preparing it for use in the later stages by enhancing the signal of interest while suppressing spurious components. Numerous approaches for preprocessing MS data have been described in the literature. In this chapter, we will describe both, standard techniques originating from classical signal and image processing, and novel computational approaches specifically tailored to the analysis of MS data sets. We will focus on low level signal processing tasks such as baseline reduction, denoising, and fe... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114745 Thu, 12 Nov 2009 00:00:00 +0100 3114745 http://www.medworm.com/index.php?rid=3114744&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60761-444-9_10 The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that ... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=3114744 Thu, 12 Nov 2009 00:00:00 +0100 3114744 http://www.medworm.com/index.php?rid=2819371&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_9 Ever-increasing size of the biomedical literature makes more precise information retrieval and tapping into implicit knowledge in scientific literature a necessity. In this chapter, first, three new variants of the expectation–maximization (EM) method for semisupervised document classification (Machine Learning 39:103–134, 2000) are introduced to refine biomedical literature meta-searches. The retrieval performance of a multi-mixture per class EM variant with Agglomerative Information Bottleneck clustering (Slonim and Tishby (1999) Agglomerative information bottleneck. In Proceedings of NIPS-12) using Davies–Bouldin cluster validity index (IEEE Transactions on Pattern Analysis and Machine Intelligence 1:224–227, 1979), rivaled the state-of-the-art transductive suppo... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819371 Mon, 03 Aug 2009 23:00:00 +0100 2819371 http://www.medworm.com/index.php?rid=2819370&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_8 In this chapter, we will focus on the role of bioinformatics to analyze a protein after its protein structure has been determined. First, we present how to validate protein structures for quality assurance. Then, we discuss how to analyze protein–protein interfaces and how to predict the biomolecule which is the biological oligomeric state of the protein. Finally, we discuss how to search for homologs based on the 3-D structure which is an essential step for understanding protein function. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819370 Mon, 03 Aug 2009 23:00:00 +0100 2819370 http://www.medworm.com/index.php?rid=2819369&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_7 The observation that similar protein sequences fold into similar three-dimensional structures provides a basis for the methods which predict structural features of a novel protein based on the similarity between its sequence and sequences of known protein structures. Similarity over entire sequence or large sequence fragment(s) enables prediction and modeling of entire structural domains while statistics derived from distributions of local features of known protein structures make it possible to predict such features in proteins with unknown structures. The accuracy of models of protein structures is sufficient for many practical purposes such as analysis of point mutation effects, enzymatic reactions, interaction interfaces of protein complexes, and active sites. Protein models are also u... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819369 Mon, 03 Aug 2009 23:00:00 +0100 2819369 http://www.medworm.com/index.php?rid=2819368&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_6 Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819368 Mon, 03 Aug 2009 23:00:00 +0100 2819368 http://www.medworm.com/index.php?rid=2819367&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_5 Discovery of DNA sequence variants responsible for human phenotypic variation is key to advances in molecular diagnostics and medicines. Historically, variants that alter the protein-coding sequence of genes have been targeted when attempting to identify a trait’s etiology; this is done because the rules governing these regions are generally well-understood and candidate variants can be easily selected. However, the effects of variants on gene regulation are increasingly regarded as being as important as protein-coding variation in uncovering the nature of phenotypic variation. I discuss resources and methodology that have recently been developed to computationally prioritize variants that may alter gene expression. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819367 Mon, 03 Aug 2009 23:00:00 +0100 2819367 http://www.medworm.com/index.php?rid=2819366&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_4 A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist to a walking trip in an attempt to stimulate interdisciplinary research. During a break, they watch a cow in a field nearby and the leader of the group asks, “I wonder how one could decide on the size of a cow?” Since a cow is a biological object, the biologist responded first: “I have seen many cows in this area and know it is a big cow.” The mathematician argued, “The true volume is determined by integrating the mathematical function that describes the outer surface of the cow’s... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819366 Mon, 03 Aug 2009 23:00:00 +0100 2819366 http://www.medworm.com/index.php?rid=2819365&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_3 This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net ) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration ove... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819365 Mon, 03 Aug 2009 23:00:00 +0100 2819365 http://www.medworm.com/index.php?rid=2819364&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_2 To promote scientific discovery and education, the federated Biomedical Informatics Research Network (BIRN) Data Repository (BDR) supports data storage, sharing, querying, and downloading for the biomedical community, enabling the integration of multiple data resources from a single entry point. The BDR encourages data sharing both for investigators requesting assistance with databasing and informatics infrastructure, and for those wishing to extend the reach of existing data resources to be registered with the BDR. Both approaches rely heavily on data integration and knowledge management techniques, ensuring capabilities for intelligent exploration of diverse data resources that make up the BDR’s shared environment. Although the development of the BDR has been driven by BIRN testbed... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819364 Mon, 03 Aug 2009 23:00:00 +0100 2819364 http://www.medworm.com/index.php?rid=2819363&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_1 Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being collected at an alarming rate. The specialization of fields in biology and medicine demonstrates the need for somewhat different structures for storage and retrieval of data. For biologists, the need for structured information and integration across a number of domains drives development. For clinical researchers and hospitals, the need for a structured medical record accessible to, ideally, any medical practitioner who might require it during the course of research or patient treatment, patient confidentiality, an... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819363 Mon, 03 Aug 2009 23:00:00 +0100 2819363 http://www.medworm.com/index.php?rid=2819362&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_12 Single Sign-On (SSO) is a practical requirement for software applications, which rely on distributed, networked services requiring authentication. SSO is as much a convenient feature for users as it is a security concern for application designers. The security requirement becomes critical in institutions that adhere to HIPPA regulations. In this chapter, we discuss SSO as it applies to a grid portal using remote computational resources and grid storage, which contain Personal Health Information (PHI). We cover the implementation of Public Key Infrastructure(PKI) to meet HIPPA security requirements such as authentication, confidentiality, nonrepudiation, and dataintegrity. Furthermore, we discuss the different technologies in PKI that solves these security concerns with respect to protectin... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819362 Mon, 03 Aug 2009 23:00:00 +0100 2819362 http://www.medworm.com/index.php?rid=2819361&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_11 The field of high-performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete various computational processes. These strategies range from the development of higher-performance hardware to the assembly of large networks of commodity computers, with each strategy designed to address a particular aspect and/or manifestation of a given computational problem. GWE (Grid Wizard Enterprise) in that regard, is an HPC distributed enterprise system, aimed at providing a solution to the particular problem of running inter-independent computational processes faster by parallelizing their execution across a virtual grid of computational resources with a minimum of user interv... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819361 Mon, 03 Aug 2009 23:00:00 +0100 2819361 http://www.medworm.com/index.php?rid=2819360&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-524-4_10 Imagination is the critical point in developing of realistic intelligence (AI) systems. One way to approach imagination would be simulation of its properties and operations. We developed two models “Brain Network Hierarchy of Languages,” and “Semantical Holographic Calculus” and simulation system ScriptWriter that emulate the process of imagination through an automatic animation of English texts. The purpose of this paper is to demonstrate the model and present “ScriptWriter” system http://nvo.sdsc.edu/NVO/JCSG/get_SRB_mime_file2.cgi//home/tamara.sdsc/test/demo.zip?F=/home/tamara.sdsc/test/demo.zip&M=application/x-gtar for simulation of the imagination. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2819360 Mon, 03 Aug 2009 23:00:00 +0100 2819360 http://www.medworm.com/index.php?rid=2364082&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_17 The analysis of DNA sequence polymorphisms and SNPs (single nucleotide polymorphisms) can provide insights into the evolutionary forces acting on populations and species. Available population-genetic methods, and particularly those based on the coalescent theory, have become the primary framework to analyze such DNA polymorphism data. Here, I explain some essential analytical methods for interpreting DNA polymorphism data and also describe the basic functionalities of the DnaSP software. DnaSP is a multi-propose program that allows conducting exhaustive DNA polymorphism analysis using a graphical user-friendly interface. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364082 Thu, 01 Jan 2009 05:00:00 +0100 2364082 http://www.medworm.com/index.php?rid=2364081&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_10 We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364081 Thu, 01 Jan 2009 05:00:00 +0100 2364081 http://www.medworm.com/index.php?rid=2364080&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_11 There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likel... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364080 Thu, 01 Jan 2009 05:00:00 +0100 2364080 http://www.medworm.com/index.php?rid=2364079&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_12 We present in this chapter a simple protocol mainly based on the combination of the program GeneID and other computational tools to annotate the location of a gene, which was previously annotated in D. melanogaster, in the recently assembled genome of D. yakuba. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364079 Thu, 01 Jan 2009 05:00:00 +0100 2364079 http://www.medworm.com/index.php?rid=2364078&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_13 Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. Eukaryotic genome annotations have improved greatly due to large-scale characterization of full-length cDNAs, transcriptional start sites (TSSs), and comparative genomics. Regulatory elements are identified in promoter regions using a variety of enumerative or alignment-based methods. Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364078 Thu, 01 Jan 2009 05:00:00 +0100 2364078 http://www.medworm.com/index.php?rid=2364077&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_14 Genomic DNA is being sequenced and annotated at a rapid rate, with terabases of DNA currently deposited in GenBank and other repositories. Genome browsers provide an essential collection of resources to visualize and analyze chromosomal DNA. The University of California, Santa Cruz (UCSC) Genome Browser provides annotations from the level of single nucleotides to whole chromosomes for four dozen metazoan and other species. The Genome Browser may be used to address a wide range of problems in bioinformatics (e.g., sequence analysis), comparative genomics, and evolution. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364077 Thu, 01 Jan 2009 05:00:00 +0100 2364077 http://www.medworm.com/index.php?rid=2364076&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_16 We present here a survey of two of the most readily available and widely used bioinformatics applications for the detection, characterization, and analysis of TE sequences in eukaryotic genomes: CENSOR and RepeatMasker. For each program, information on availability, input, output, and the algorithmic methods used is provided. Specific examples of the use of CENSOR and RepeatMasker are also described. CENSOR and RepeatMasker both rely on homology-based methods for the detection of TE sequences. There are several other classes of methods available for the analysis of repetitive DNA sequences including de novo methods that compare genomic sequences against themselves, class-specific methods that use structural characteristics of specific classes of elements to aid in their identification, and... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364076 Thu, 01 Jan 2009 05:00:00 +0100 2364076 http://www.medworm.com/index.php?rid=2364075&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_15 Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and the association of heritable traits with underlying genetic variation. The development of high-throughput methods for the detection of single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) has led to a revolution in their use as molecular markers. The availability of large sequence data sets permits mining for these molecular markers, which may then be used for applications such as genetic trait mapping, diversity analysis and marker assisted selection in agriculture. Here we describe web-based automated methods for the discovery of SSRs using SSR taxonomy tree, the discovery of SNPs from sequence data using SNPServer and the identification of validated SNPs from within th... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364075 Thu, 01 Jan 2009 05:00:00 +0100 2364075 http://www.medworm.com/index.php?rid=2364074&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_1 Similarity searches are an essential component of most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In this chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364074 Thu, 01 Jan 2009 05:00:00 +0100 2364074 http://www.medworm.com/index.php?rid=2364073&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_2 OrthologID ( http://nypg.bio.nyu.edu/orthologid/ ) allows for the rapid and accurate identification of gene orthology within a character-based phylogenetic framework. The Web application has two functions – an orthologous group search and a query orthology classification. The former determines orthologous gene sets for complete genomes and identifies diagnostic characters that define each orthologous gene set; and the latter allows for the classification of unknown query sequences to orthology groups. The first module of the Web application, the gene family generator, uses an E-value based approach to sort genes into gene families. An alignment constructor then aligns members of gene families and the resulting gene family alignments are submitted to the tree b... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364073 Thu, 01 Jan 2009 05:00:00 +0100 2364073 http://www.medworm.com/index.php?rid=2364072&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_3 Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364072 Thu, 01 Jan 2009 05:00:00 +0100 2364072 http://www.medworm.com/index.php?rid=2364071&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_4 Compositional heterogeneity is a poorly appreciated attribute of aligned nucleotide and amino acid sequences. It is a common property of molecular phylogenetic data, and it has been found to occur across sequences and/or across sites. Most molecular phylogenetic methods assume that the sequences have evolved under globally stationary, reversible, and homogeneous conditions, implying that the sequences should be compositionally homogeneous. The presence of the above-mentioned compositional heterogeneity implies that the sequences must have evolved under more general conditions than is commonly assumed. Consequently, there is a need for reliable methods to detect under what conditions alignments of nucleotides or amino acids may have evolved. In this chapter, we describe one such program. Se... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364071 Thu, 01 Jan 2009 05:00:00 +0100 2364071 http://www.medworm.com/index.php?rid=2364070&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_5 jModelTest is a bioinformatic tool for choosing among different models of nucleotide substitution. The program implements five different model selection strategies, including hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a performance-based decision theory method (DT). The output includes estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates, including model-averaged phylogenies. jModelTest is a Java program that runs under Mac OSX, Windows, and Unix systems with a Java Run Environment installed, and it can be freely downloaded from http://darwin.uvigo.es . (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364070 Thu, 01 Jan 2009 05:00:00 +0100 2364070 http://www.medworm.com/index.php?rid=2364069&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_6 Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion are usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenies is computationally demanding, and careful examination ... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364069 Thu, 01 Jan 2009 05:00:00 +0100 2364069 http://www.medworm.com/index.php?rid=2364068&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_7 We describe the most widely used supertree methods implemented in the software program “clann” and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at http://bioinf.nuim.ie/software/clann . (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364068 Thu, 01 Jan 2009 05:00:00 +0100 2364068 http://www.medworm.com/index.php?rid=2364067&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_8 Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest of the population, or increases its genetic diversity, and negative selection removes those alleles that are deleterious. Codon-based models of molecular evolution are able to infer signatures of selection from alignments of homologous sequences by estimating the relative rates of synonymous (dS) and non-synonymous substitutions (dN). Datamonkey ( http://www.datamonkey.org ) provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in t... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364067 Thu, 01 Jan 2009 05:00:00 +0100 2364067 http://www.medworm.com/index.php?rid=2364066&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-251-9_9 Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. While its evolutionary value is a matter of quite intense debate, so too is the influence of recombination on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. The crux of the problem is that when nucleic acids recombine, the daughter or recombinant molecules no longer have a single evolutionary history. All analysis methods that derive increased power from correctly inferring evolutionary relationships between sequences will therefore be at least mildly sensitive to the effects of recombination. The importance of considering recombination in evolutionary studies is underlined by the bewildering array of currently available methods an... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364066 Thu, 01 Jan 2009 05:00:00 +0100 2364066 http://www.medworm.com/index.php?rid=2364090&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_17 Enzymes play central roles in metabolic pathways, and the prediction of metabolic pathways in newly sequenced genomes usually starts with the assignment of genes to enzymatic reactions. However, genes with similar catalytic activity are not necessarily similar in sequence, and therefore the traditional sequence similarity-based approach often fails to identify the relevant enzymes, thus hindering efforts to map the metabolome of an organism. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364090 Tue, 01 Jul 2008 04:00:00 +0100 2364090 http://www.medworm.com/index.php?rid=2364089&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_18 Intricate networks of protein interactions rely on the ability of a protein to recognize its targets: other proteins, ligands, and sites on DNA and RNA. To recognize other molecules, it was suggested that a protein uses a small set of specificity-determining residues (SDRs). How can one find these residues in proteins and distinguish them from other functionally important amino acids? A number of bioinformatics methods to predict SDRs have been developed in recent years. These methods use genomic information and multiple sequence alignments to identify positions exhibiting a specific pattern of conservation and variability. The challenge is to delineate the evolutionary pattern of SDRs from that of the active site residues and the residues responsible for formation of the protein’s s... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364089 Tue, 01 Jul 2008 04:00:00 +0100 2364089 http://www.medworm.com/index.php?rid=2364088&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_19 Understanding how mutations lead to changes in protein function and/or protein interaction is critical to understanding the molecular causes of clinical phenotypes. In this method, we present a path toward integration of protein interaction data and mutation data and then demonstrate the identification of a subset of proteins and interactions that are important to a particular disease. We then build a statistical model of disease mutations in this disease-associated subset of proteins, and visualize these results. Using Alzheimer’s disease (AD) as case implementation, we find that we are able to identify a subset of proteins involved in AD and discriminate disease-associated mutations from SNPs in these proteins with 83% accuracy. As the molecular causes of disease become more unders... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364088 Tue, 01 Jul 2008 04:00:00 +0100 2364088 http://www.medworm.com/index.php?rid=2364087&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_20 Gene networks have proven to be an effective approach for modeling cellular systems, capable of capturing some of the extreme complexity of cells in a formal theoretical framework. Not surprisingly, this complexity, combined with our still-limited amount of experimental data measuring the genes and their interactions, makes the reconstruction of gene networks difficult. One powerful strategy has been to analyze functional genomics data using supervised learning of network relationships based upon reference examples from our current knowledge. However, this reliance on the set of reference examples for the supervised learning can introduce major pitfalls, with misleading reference sets resulting in suboptimal learning. There are three requirements for an effective reference set: comprehensi... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364087 Tue, 01 Jul 2008 04:00:00 +0100 2364087 http://www.medworm.com/index.php?rid=2364086&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_21 Clustering is a popular technique commonly used to search for groups of similarly expressed genes using mRNA expression data. There are many different clustering algorithms and the application of each one will usually produce different results. Without additional evaluation, it is difficult to determine which solutions are better. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364086 Tue, 01 Jul 2008 04:00:00 +0100 2364086 http://www.medworm.com/index.php?rid=2364085&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_22 The Bioverse is a framework for creating, warehousing and presenting biological information based on hierarchical levels of organisation. The framework is guided by a deeper philosophy of desiring to represent all relationships between all components of biological systems towards the goal of a wholistic picture of organismal biology. Data from various sources are combined into a single repository and a uniform interface is exposed to access it. The power of the approach of the Bioverse is that, due to its inclusive nature, patterns emerge from the acquired data and new predictions are made. The implementation of this repository (beginning with acquisition of source data, processing in a pipeline, and concluding with storage in a relational database) and interfaces to the data contained in ... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364085 Tue, 01 Jul 2008 04:00:00 +0100 2364085 http://www.medworm.com/index.php?rid=2364084&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_24 Attaining a detailed understanding of the various biological networks in an organism lies at the core of the emerging discipline of systems biology. A precise description of the relationships formed between genes, mRNA molecules, and proteins is a necessary step toward a complete description of the dynamic behavior of an organism at the cellular level, and toward intelligent, efficient, and directed modification of an organism. The importance of understanding such regulatory, signaling, and interaction networks has fueled the development of numerous in silico inference algorithms, as well as new experimental techniques and a growing collection of public databases. The Software Environment for BIological Network Inference (SEBINI) has been created to provide an interactive environment for t... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364084 Tue, 01 Jul 2008 04:00:00 +0100 2364084 http://www.medworm.com/index.php?rid=2364083&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_23 Integration of large and diverse biological data sets is a daunting problem facing systems biology researchers. Exploring the complex issues of data validation, integration, and representation, we present a systematic approach for the management and analysis of large biological data sets based on data warehouses. Our system has been implemented in the Bioverse, a framework combining diverse protein information from a variety of knowledge areas such as molecular interactions, pathway localization, protein structure, and protein function. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2364083 Tue, 01 Jul 2008 04:00:00 +0100 2364083 http://www.medworm.com/index.php?rid=2506219&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_10 Analysis of expression quantitative trait loci (eQTL) helps elucidate the connection between genotype, gene expression levels, and phenotype. However, standard statistical genetics can only attribute the changes in expression levels to loci on the genome, not specific genes. Each locus can contain many genes, making it very difficult to discover which gene is controlling the expression levels of other genes. Furthermore, it is even more difficult to find a pathway of molecular interactions responsible for controlling the expression levels. Here we describe a series of techniques for finding explanatory pathways by exploring the graphs of molecular interactions. We show several simple methods can find complete pathways that explain the mechanism of differential expression in eQTL data. (Sou... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506219 Mon, 30 Jun 2008 23:00:00 +0100 2506219 http://www.medworm.com/index.php?rid=2506218&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_7 Spatially or chemically isolated modules that carry out discrete functions are considered fundamental building blocks of cellular organization. However, detecting them in highly integrated biological networks requires a thorough understanding of the organization of these networks. In this chapter I argue that many biological networks are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units. On top of a scale-free degree distribution, these networks show a power law scaling of the clustering coefficient with the node degree, a property that can be used as a signature of hierarchical organization. As a case study, I identify the hierarchical modules within the Escherichia coli metabolic network, and show that the... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506218 Mon, 30 Jun 2008 23:00:00 +0100 2506218 http://www.medworm.com/index.php?rid=2506217&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_6 We describe how to compile and handle various formats and identifiers of data sets from different sources and how to predict TRIs using a homology-based approach, utilizing the compiled data sets. Integrated data sets include experimentally verified TRIs, binding sites of transcription factors, promoter sequences, protein subcellular localization, and protein families. Predicted TRIs expand the networks of gene regulation for a large number of organisms. The integration of experimentally verified and predicted TRIs with other known protein–protein interactions (PPIs) gives insight into specific pathways, network motifs, and the topological dynamics of an integrated network with gene expression under different conditions, essential for exploring functional genomics and systems biology... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506217 Mon, 30 Jun 2008 23:00:00 +0100 2506217 http://www.medworm.com/index.php?rid=2506216&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_5 Accurate mapping of protein–protein interaction networks in model organisms is a crucial first step toward subsequent quantitative study of the organization and evolution of biological systems. Data quality of experimental interactome maps can be assessed and improved by integrating multiple sources of evidence using machine learning methods. Here we describe the commonly used algorithms for predicting protein–protein interaction by genome data integration, and discuss several important yet often overlooked issues in computational reconstruction of protein–protein interaction networks. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506216 Mon, 30 Jun 2008 23:00:00 +0100 2506216 http://www.medworm.com/index.php?rid=2506215&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_4 The concept of molecular co-evolution drew attention in recent years as the basis for several algorithms for the prediction of protein–protein interactions. While being successful on specific data, the concept has never been tested on a large set of proteins. In this chapter we analyze the feasibility of the co-evolution principle for protein–protein interaction prediction through one of its derivatives, the correlated divergence model. Given two proteins, the model compares the patterns of divergence of their families and assigns a score based on the correlation between the two. The working hypothesis of the model postulates that the stronger the correlation the more likely is that the two proteins interact. Several novel variants of this model are considered, including algori... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506215 Mon, 30 Jun 2008 23:00:00 +0100 2506215 http://www.medworm.com/index.php?rid=2506214&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_3 The ever accumulating wealth of knowledge about protein interactions and the domain architecture of involved proteins in different organisms offers ways to understand the intricate interplay between interactome and proteome. Ultimately, the combination of these sources of information will allow the prediction of interactions among proteins where only domain composition is known. Based on the currently available protein–protein interaction and domain data of Saccharomyces cerevisiae and Drosophila melanogaster we introduce a novel method, Maximum Specificity Set Cover (MSSC), to predict potential protein–protein interactions. Utilizing interactions and domain architectures of domains as training sets, this algorithm employs a set cover approach to partition domain pairs, which a... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506214 Mon, 30 Jun 2008 23:00:00 +0100 2506214 http://www.medworm.com/index.php?rid=2506213&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_2 We present an all-atom molecular modeling method that can predict the binding specificity of a transcription factor based on its 3D structure, with no further information required. We use molecular dynamics and free energy calculations to compute the relative binding free energies for a transcription factor with multiple possible DNA sequences. These sequences are then used to construct a position weight matrix to represent the transcription factor–binding sites. Free energy differences are calculated by morphing one base pair into another using a multi-copy representation in which multiple base pairs are superimposed at a single DNA position. Water-mediated hydrogen bonds between transcription factor side chains and DNA bases are known to contribute to binding specificity for certai... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506213 Mon, 30 Jun 2008 23:00:00 +0100 2506213 http://www.medworm.com/index.php?rid=2506212&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-243-4_1 Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology–derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=2506212 Mon, 30 Jun 2008 23:00:00 +0100 2506212 http://www.medworm.com/index.php?rid=1740064&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-429-6_1 The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from “Unified Nucleic Acid Folding.” Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures,... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1740064 Thu, 01 May 2008 04:00:00 +0100 1740064 http://www.medworm.com/index.php?rid=1607092&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_9 In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter reviews the data, methodology, and technical challenges of these genome-wide analyses of alternative splicing, and briefly surveys some of the uses to which such alternative splicing databases have been put. For example, with proper alternative splicing database schema design, it is possible to query genome-wide for alternative splicing patterns that are specific to particular tissues, disease states (e.g., cancer), gender, or developmental stages. EST alignments can be used to estimate exon inclusion or exclusion level of... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607092 Thu, 01 May 2008 04:00:00 +0100 1607092 http://www.medworm.com/index.php?rid=1607091&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_8 Gene-finding is concerned with the identification of stretches of DNA in a genomic sequence that encode biologically active products, such as proteins or functional non-coding RNAs. This is usually the first step in the analysis of any novel piece of genomic sequence, which makes it a very important issue, as all downstream analyses depend on the results. This chapter focuses on the biological basis, computational approaches, and corresponding programs that are available for the automated identification of protein-coding genes. For prokaryotic and eukaryotic genomes, as well as the novel, multi-species sequence data originating from environmental community studies, the state of the art in automated gene finding is described. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607091 Thu, 01 May 2008 04:00:00 +0100 1607091 http://www.medworm.com/index.php?rid=1607090&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_7 Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments. It should be stressed, however, that many complex biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, so that th... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607090 Thu, 01 May 2008 04:00:00 +0100 1607090 http://www.medworm.com/index.php?rid=1607089&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_6 The dynamic structure and functions of genomes are being revealed simultaneously with the progress of genome analyses. Evidence indicating genome regional characteristics (genome annotations in a broad sense) provide the basis for further analyses. Target listing and screening can be effectively performed in silico using such data. This chapter describes steps to obtain publicly available genome annotations or construct new annotations based on your own analyses, as well as an overview of the types of available genome annotations and corresponding resources. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607089 Thu, 01 May 2008 04:00:00 +0100 1607089 http://www.medworm.com/index.php?rid=1607088&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_5 In recent years, biological ontologies have emerged as a means of representing and organizing biological concepts, enabling biologists, bioinformaticians, and others to derive meaning from large datasets. This chapter provides an overview of formal principles and practical considerations of ontology construction and application. Ontology development concepts are illustrated using examples drawn from the Gene Ontology (GO) and other OBO ontologies. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607088 Thu, 01 May 2008 04:00:00 +0100 1607088 http://www.medworm.com/index.php?rid=1607087&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_4 Microarrays have become a widely used technology in molecular biology research. One of their main uses is to measure gene expression. Compared to older expression measuring assays such as Northern blotting, analyzing gene expression data from microarrays is inherently more complex due to the massive amounts of data they produce. The analysis of microarray data requires biologists to collaborate with bioinformaticians or learn the basics of statistics and programming. Many software tools for microarray data analysis are available. Currently one of the most popular and freely available software tools is Bioconductor. This chapter uses Bioconductor to preprocess microarray data, detect differentially expressed genes, and annotate the gene lists of interest. (Source: Springer protocols feed by... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607087 Thu, 01 May 2008 04:00:00 +0100 1607087 http://www.medworm.com/index.php?rid=1607086&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_3 X-ray biocrystallography is the most powerful method to obtain a macromolecular structure. The improvement of computational technologies in recent years and the development of new and powerful computer programs together with the enormous increment in the number of protein structures deposited in the Protein Data Bank, render the resolution of new structures easier than in the past. The aim of this chapter is to provide practical procedures useful for solving a new structure. It is impossible to give more than a flavor of what the x-ray crystallographic technique entails in one brief chapter; therefore, this chapter focuses its attention on the Molecular Replacement method. Whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set an... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607086 Thu, 01 May 2008 04:00:00 +0100 1607086 http://www.medworm.com/index.php?rid=1607085&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_24 This chapter surveys the use of fixed-parameter algorithms in phylogenetics. A central computational problem in this field is the construction of a likely phylogeny (genealogical tree) for a set of species based on observed differences in the phenotype, differences in the genotype, or given partial phylogenies. Ideally, one would like to construct so-called perfect phylogenies, which arise from an elementary evolutionary model, but in practice one must often be content with phylogenies whose “distance from perfection” is as small as possible. The computation of phylogenies also has applications in seemingly unrelated areas such as genomic sequencing and finding and understanding genes. The numerous computational problems arising in phylogenetics are often NP-complete, but for m... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607085 Thu, 01 May 2008 04:00:00 +0100 1607085 http://www.medworm.com/index.php?rid=1607084&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_23 The historical movement of organisms, whether recent or in the distant past, forms a central aspect of evolutionary studies. Inferring patterns of migration can be difficult and requires reliance on a large suite of bioinformatic tools. As it is primarily the movement of groups of related individuals or populations that are of interest, population genetic and phylogeographic methods form the core of tools used to decipher migration patterns. Following a description of these tools, we discuss the most critical—and potentially most difficult—aspect of these studies: the inference process used. Designing a study, determining which data to collect, how to analyze the data, and how to coordinate these results into a coherent narrative are all a part of this inference process. Furthe... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607084 Thu, 01 May 2008 04:00:00 +0100 1607084 http://www.medworm.com/index.php?rid=1607083&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_22 Recombination is the major motor of evolution. While mutations result in gradual changes, recombination reshuffles entire functional modules and thus progresses evolution in leaps and bounds. We need to identify recombination breakpoints in sequences to understand the evolutionary process, the impact of recombination, and to reconstruct the phylogenetic history of genes and genomes. This chapter provides a step by step guide for detecting recombination even in large and complex sequence alignments. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607083 Thu, 01 May 2008 04:00:00 +0100 1607083 http://www.medworm.com/index.php?rid=1607082&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_21 Nucleotide sequences of microbial genomes provide evidence that genes have been shared among organisms, a phenomenon known as lateral genetic transfer (LGT). Hypotheses about the importance of LGT in the evolution and diversification of microbes can be tested by analyzing the extensive quantities of sequence data now available. Some analysis methods identify genes with sequence features that differ from those of the surrounding genome, whereas other methods are based on inference and comparison of phylogenetic trees. A large-scale search for LGT in 144 genomes using phylogenetic methods has revealed that although parent-to-offspring (“vertical”) inheritance has been the dominant mode of gene transmission, LGT has nonetheless been frequent, especially among organisms that are cl... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607082 Thu, 01 May 2008 04:00:00 +0100 1607082 http://www.medworm.com/index.php?rid=1607081&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_20 The chromosomes of mammalian genomes exhibit reasonably high levels of similarity that can be used to study small-scale sequence variations. A different approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene or segment orders. This chapter describes three computational tools (GRIMM-Synteny, GRIMM, and MGR) that can be used separately or in succession to contrast different organisms at the genome-level to exploit large-scale rearrangements as a phylogenetic character. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607081 Thu, 01 May 2008 04:00:00 +0100 1607081 http://www.medworm.com/index.php?rid=1607080&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_2 This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint ... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607080 Thu, 01 May 2008 04:00:00 +0100 1607080 http://www.medworm.com/index.php?rid=1607079&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_19 With the recent sequencing of numerous complete genomes and the advent of high throughput technologies (e.g., yeast two-hybrid assays or tandem-affinity purification experiments), it is now possible to estimate the ancestral form of protein interaction networks. This chapter combines protein interaction data and comparative genomics techniques in an attempt to reconstruct a network of core proteins and interactions in yeast that potentially represents an ancestral state of the budding yeast protein interaction network. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607079 Thu, 01 May 2008 04:00:00 +0100 1607079 http://www.medworm.com/index.php?rid=1607078&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_18 The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a general mix of linear and circular chromosomes. In the general case the menu includes: inversion, translocation, transposition, formation and absorption of circular intermediates, conversion between linear and circular chromosomes, block interchange, fission, and fusion. This chapter discusses the well-known edge graph and its dual, the adjacency graph, recently introduced by Bergeron et al. Step-by-step procedures are given for constructing and manipulating these graphs. Simple algorithms are given in the ad... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607078 Thu, 01 May 2008 04:00:00 +0100 1607078 http://www.medworm.com/index.php?rid=1607077&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_17 To explain the evolutionary mechanisms by which populations of organisms change over time, it is necessary to first understand the pathways by which genomes have changed over time. Understanding genome evolution requires comparing modern genomes with ancestral genomes, which thus necessitates the reconstruction of those ancestral genomes. This chapter describes automated approaches to infer the nature of ancestral genomes from modern sequenced genomes. Because several rounds of whole genome duplication have punctuated the evolution of animals with backbones, and current methods for ortholog calling do not adequately account for such events, we developed ways to infer the nature of ancestral chromosomes after genome duplication. We apply this method here to reconstruct the ancestors of a sp... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607077 Thu, 01 May 2008 04:00:00 +0100 1607077 http://www.medworm.com/index.php?rid=1607076&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_16 Most phylogenetic methods are model-based and depend on Markov models designed to approximate the evolutionary rates between nucleotides or amino acids. When Markov models are selected for analysis of alignments of these characters, it is assumed that they are close approximations of the evolutionary processes that gave rise to the data. A variety of methods have been developed for estimating the fit of Markov models, and some of these methods are now frequently used for the selection of Markov models. In a growing number of cases, however, it appears that the investigators have used the model-selection methods without acknowledging their inherent shortcomings. This chapter reviews the issue of model selection and model evaluation. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607076 Thu, 01 May 2008 04:00:00 +0100 1607076 http://www.medworm.com/index.php?rid=1607075&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_15 Methods to detect the action of selection on proteins can now make strong predictions about its strength and location, but are becoming increasingly technical. The complexity of the methods makes it difficult to determine and interpret the significance of any selection detected. With more information being extracted from the data, the quality of the protein alignment and phylogeny used becomes increasingly important in assessing whether or not a prediction is merely a statistical artifact. Both data quality issues and statistical assessment of the results are considered. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607075 Thu, 01 May 2008 04:00:00 +0100 1607075 http://www.medworm.com/index.php?rid=1607074&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_14 Molecular phylogenetics examines how biological sequences evolve and the historical relationships between them. An important aspect of many such studies is the estimation of a phylogenetic tree, which explicitly describes evolutionary relationships between the sequences. This chapter provides an introduction to evolutionary trees and some commonly used inferential methodology, focusing on the assumptions made and how they affect an analysis. Detailed discussion is also provided about some common algorithms used for phylogenetic tree estimation. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and maximum likelihood phylogenetics. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607074 Thu, 01 May 2008 04:00:00 +0100 1607074 http://www.medworm.com/index.php?rid=1607073&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_13 DNA and amino acid sequences contain information about both the phylogenetic relationships among species and the evolutionary processes that caused the sequences to divergence. Mathematical and statistical methods try to detect this information to determine how and why DNA and protein molecules work the way they do. This chapter describes some of the models of evolution of biological sequences most widely used. It first focuses on single nucleotide/amino acid replacement rate models. Then it discusses the modelling of evolution at gene and protein module levels. The chapter concludes with speculations about the future use of molecular evolution studies using genomic and proteomic data. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607073 Thu, 01 May 2008 04:00:00 +0100 1607073 http://www.medworm.com/index.php?rid=1607072&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_12 Sequence motif discovery algorithms are an important part of the computational biologist's toolkit. The purpose of motif discovery is to discover patterns in biopolymer (nucleotide or protein) sequences in order to better understand the structure and function of the molecules the sequences represent. This chapter provides an overview of the use of sequence motif discovery in biology and a general guide to the use of motif discovery algorithms. The chapter discusses the types of biological features that DNA and protein motifs can represent and their usefulness. It also defines what sequence motifs are, how they are represented, and general techniques for discovering them. The primary focus is on one aspect of motif discovery: discovering motifs in a set of unaligned DNA or protein sequences... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607072 Thu, 01 May 2008 04:00:00 +0100 1607072 http://www.medworm.com/index.php?rid=1607071&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_11 Whole-genome comparisons among mammalian and other eukaryotic organisms have revealed that they contain large quantities of conserved non—protein-coding sequence. Although some of the functions of this non-coding DNA have been identified, there remains a large quantity of conserved genomic sequence that is of no known function. Moreover, the task of delineating the conserved sequences is non-trivial, particularly when some sequences are conserved in only a small number of lineages. Sequence segmentation is a statistical technique for identifying putative functional elements in genomes based on atypical sequence characteristics, such as conservation levels relative to other genomes, GC content, SNP frequency, and potentially many others. The publicly available program changept and ass... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607071 Thu, 01 May 2008 04:00:00 +0100 1607071 http://www.medworm.com/index.php?rid=1607070&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_10 Most alternative splicing events in human and other eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as EST sequencing and oligonu-cleotide microarrays. Reconstructing full-length transcript isoforms from such sequence fragments is a major interest and challenge for computational analyses of pre-mRNA alternative splicing. This chapter describes a general graph-based approach for computational inference of full-length isoforms. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607070 Thu, 01 May 2008 04:00:00 +0100 1607070 http://www.medworm.com/index.php?rid=1607069&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-159-2_1 Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSD (International Nucleotide Sequence Database—DDBJ/EMBL/GenBank) is an international, centralized primary sequence resource that is freely available on the internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter summarizes the nucleotide sequence database resources, provides information on how to submit sequences to the databases, and explains how to access the sequence data. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1607069 Thu, 01 May 2008 04:00:00 +0100 1607069 http://www.medworm.com/index.php?rid=1539257&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_11 Three-dimensional analysis of protein structures is proving to be one of the most fruitful modes of biological and medical discovery in the early 21st century, providing fundamental insight into many (perhaps most) biochemical functions of relevance to the cause and treatment of diseases. Fully realizing such insight, however, would require analysis of too many distinct proteins for thorough laboratory analysis of all proteins to be feasible, thus, any method capable of accurate, efficient in silico structure prediction should prove highly expeditious. The technique generally acknowledged to provide the most accurate protein structure predictions, called comparative modeling, has, thus, attracted substantial attention and is the focus of this chapter. Although other reviews have reported o... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539257 Fri, 04 Apr 2008 04:00:00 +0100 1539257 http://www.medworm.com/index.php?rid=1539256&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_18 An important contribution to today's computer-aided drug design is the automated screening of large compound databases against structurally resolved protein receptors targets. The introduction of ligand flexibility has, by now, become a standardized procedure. In contrast, a general approach to treat target degrees of freedom is still to be found, a consequence of the extreme increase of computational complexity, which comes along with the relaxation of protein degrees of freedom. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539256 Fri, 04 Apr 2008 04:00:00 +0100 1539256 http://www.medworm.com/index.php?rid=1539255&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_10 Implicit models of membrane environments offer computational advantages in simulations of membrane-interacting proteins and peptides. Such methods are especially useful for studies of long time scale processes, such as folding and aggregation, or very large complexes that are otherwise intractable with explicit lipid environments. Implicit models replace explicit solute—solvent interactions with a mean-field approach. In the most physical models, continuum dielectric electrostatics is combined with empirical formulations for the nonpolar components of the free energy of solvation. The practical use of a number of implicit membrane models ranging from the empirical IMM1 method to generalized Born-based methods with two-dielectric and multidielectric representations of biological membr... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539255 Fri, 04 Apr 2008 04:00:00 +0100 1539255 http://www.medworm.com/index.php?rid=1539254&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_5 Normal mode analysis and essential dynamics analysis are powerful methods used for the analysis of collective motions in biomolecules. Their application has led to an appreciation of the importance of protein dynamics in function and the relationship between structure and dynamical behavior. In this chapter, the methods and their implementation are introduced and recent developments such as elastic networks and advanced sampling techniques are described. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539254 Fri, 04 Apr 2008 04:00:00 +0100 1539254 http://www.medworm.com/index.php?rid=1539253&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_14 Conformational changes are the hallmarks of protein dynamics and are often intimately related to protein functions. Molecular dynamics (MD) simulation is a powerful tool to study the time-resolved properties of protein structure in atomic details. In this chapter, we discuss the various applications of MD simulation to the study of protein conformational changes, and introduce several selected advanced techniques that may significantly increase the sampling efficiencies, including locally enhanced sampling (LES), and grow-to-fit molecular dynamics (G2FMD). (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539253 Fri, 04 Apr 2008 04:00:00 +0100 1539253 http://www.medworm.com/index.php?rid=1539252&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_17 The availability of three-dimensional (3D) models of both drug leads (small molecule ligands) and drug targets (proteins) is essential to molecular docking and computational drug discovery. This chapter describes an emerging methodology that can be used to identify both drug leads and drug targets using three newly developed web-accessible databases: 1) DrugBank; 2) The Human Metabolome Database; and 3) PubChem. Specifically, it illustrates how putative drug targets and drug leads for exogenous diseases (i.e., infectious diseases) can be readily identified and their 3D structures selected using only the genomic sequences from pathogenic bacteria or viruses as input. It also illustrates how putative drug targets and drug leads for endogenous diseases (i.e., non-infectious diseases or chroni... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539252 Fri, 04 Apr 2008 04:00:00 +0100 1539252 http://www.medworm.com/index.php?rid=1539251&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_1 Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail—literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary har... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539251 Fri, 04 Apr 2008 04:00:00 +0100 1539251 http://www.medworm.com/index.php?rid=1539250&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_13 Nuclear magnetic resonance (NMR) has become a well-established method to characterize the structures of biomolecules in solution. High-quality structures are now produced, thanks to both experimental and computational developments, allowing the use of new NMR parameters and improved protocols and force fields in structure calculation and refinement. In this chapter, we give a short overview of the various types of NMR data that can provide structural information, and then focus on the structure calculation methodology itself. We discuss and illustrate with tutorial examples both “classical” structure calculation and refinement approaches as well as more recently developed protocols for modeling biomolecular complexes. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539250 Fri, 04 Apr 2008 04:00:00 +0100 1539250 http://www.medworm.com/index.php?rid=1539249&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_9 This chapter discusses the practical aspects of setting up molecular dynamics simulations for membrane-associated proteins and peptides. Special emphasis lies on the analysis of such systems. The main focus is the association between a cationic peptide and an anionic lipid bilayer—a peptide/lipid—bilayer system—but the extension onto more complicated systems is discussed. Topology files for selected lipids and several new analysis tools relevant for protein—membrane simulations are presented, the most important ones of which are: g_helixaxis, to calculate the axis of a helix and its angle with the bilayer; g_arom, to calculate aromatic order parameters; and g_under, to calculate which lipids interact with the protein. A procedure is explained to calculate properties... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539249 Fri, 04 Apr 2008 04:00:00 +0100 1539249 http://www.medworm.com/index.php?rid=1539248&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_15 Computational protein folding can be classified into pathway and sampling approaches. Here, we use the AMBER simulation package as an example to illustrate the protocols for all-atom molecular simulations of protein folding, including system setup, simulation, and analysis. We introduced two traditional pathway approaches: ab inito folding and high-temperature unfolding. The popular replica exchange method was chosen to represent sampling approaches. Our emphasis is placed on the analysis of the simulation trajectories, and some in-depth discussions are provided for commonly encountered problems. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539248 Fri, 04 Apr 2008 04:00:00 +0100 1539248 http://www.medworm.com/index.php?rid=1539247&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_12 Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simulations of α-helical transmembrane bundles in an explicit lipid bilayer/water environment. The procedure uses a systematic conformational search of the helix rotation with experimentally constrained MDs simulations. The experimentally determined helix tilt and rotational angle of a labeled residue with site-specific infrared dichroism allows us to select a unique high-resolution model from a number of possible energy minima encountered in the systematic conformational search. (Source: Springer protocols feed by Bioi... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539247 Fri, 04 Apr 2008 04:00:00 +0100 1539247 http://www.medworm.com/index.php?rid=1539246&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_7 Selected applications of free energy calculations to the realm of membrane proteins are reviewed. The theoretical underpinnings of these calculations are described, focusing on free energy perturbation and the use of thermodynamic integration to determine free energy changes along well—delineated order parameters. Current strategies for improving the reliability of free energy calculations, while making them somewhat more affordable are outlined. Application of the free energy methodology to understand the structure and function of membrane proteins is illustrated in three concrete examples: The binding of an agonist ligand to a G protein—coupled receptor, the assisted transport of a small permeant through a membrane channel, and the recognition and association of transmembrane... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539246 Fri, 04 Apr 2008 04:00:00 +0100 1539246 http://www.medworm.com/index.php?rid=1539245&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_16 A short review of the results of molecular modeling of prion disease is presented in this chapter. According to the “one-protein theory” proposed by Prusiner, prion proteins are misfolded naturally occurring proteins, which, on interaction with correctly folded proteins may induce misfolding and propagate the disease, resulting in insoluble amyloid aggregates in cells of affected specimens. Because of experimental difficulties in measurements of origin and growth of insoluble amyloid aggregations in cells, theoretical modeling is often the only one source of information regarding the molecular mechanism of the disease. Replica exchange Monte Carlo simulations presented in this chapter indicate that proteins in the native state, N, on interaction with an energetically higher str... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539245 Fri, 04 Apr 2008 04:00:00 +0100 1539245 http://www.medworm.com/index.php?rid=1539244&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_3 A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral—free en... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539244 Fri, 04 Apr 2008 04:00:00 +0100 1539244 http://www.medworm.com/index.php?rid=1539243&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_6 Reliable first-principles calculations of protein—ligand binding constants can play important roles in the study and characterization of biological recognition processes and applications to drug discovery. A detailed procedure for such a calculation is outlined in this chapter. The methodology is computationally implemented using the molecular dynamics sampling of relevant configurational spaces and free energy perturbation techniques. The procedure is illustrated with the model system of the phosphotyrosine peptide binding to the Src SH2 domain. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539243 Fri, 04 Apr 2008 04:00:00 +0100 1539243 http://www.medworm.com/index.php?rid=1539242&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_4 In the context of molecular dynamics simulations of proteins, the term “force field” refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to s... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539242 Fri, 04 Apr 2008 04:00:00 +0100 1539242 http://www.medworm.com/index.php?rid=1539241&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_19 Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand—protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter dis... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539241 Fri, 04 Apr 2008 04:00:00 +0100 1539241 http://www.medworm.com/index.php?rid=1539240&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_2 A description of Monte Carlo methods for simulation of proteins is given. Advantages and disadvantages of the Monte Carlo approach are presented. The theoretical basis for calculating equilibrium properties of biological molecules by the Monte Carlo method is presented. Some of the standard and some of the more recent ways of performing Monte Carlo on proteins are presented. A discussion of the estimation of errors in properties calculated by Monte Carlo is given. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539240 Fri, 04 Apr 2008 04:00:00 +0100 1539240 http://www.medworm.com/index.php?rid=1539239&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-59745-177-2_8 Membrane protein structures are underrepresented in the Protein Data Bank (PDB) because of difficulties associated with expression and crystallization. As such, it is one area in which computational studies, particularly molecular dynamics (MD), can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, although not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membran... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539239 Fri, 04 Apr 2008 04:00:00 +0100 1539239 http://www.medworm.com/index.php?rid=1539263&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_11 Increasingly, the molecular genetics laboratory has to assess the biological significance of changes (variants) in a DNA sequence. Using the large genes BRCA1 and BRCA2 as examples, some approaches used to determine the biological significance of DNA variants are described. These include the characterization of the variant through a review of the literature and the various databases to assess if it has previously been described. Potential difficulties with the various databases that are available are described. Other considerations include the co-inheritance of the variant with other DNA changes, and its evolutionary conservation. Determining the possible effect of the variant on protein function is described in terms of the Grantham assessment as well as identifying functional domains. St... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539263 Fri, 21 Dec 2007 05:00:00 +0100 1539263 http://www.medworm.com/index.php?rid=1539262&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_6 Perturbations in genes play a key role in the pathogenesis of cancer. Microarray-based technology is an ideal way in which to study the effects and interactions of multiple genes in cancer. There are many technologic challenges in running a microarray study, including annotation of genes likely to be involved, designing the appropriate experiment, and ensuring adequate quality assurance steps are implemented. Once data are normalized, they need to be analyzed; and for this, there are numerous software packages and approaches. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539262 Fri, 21 Dec 2007 05:00:00 +0100 1539262 http://www.medworm.com/index.php?rid=1539261&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_1 Complex diseases can involve the interaction of multiple genes and environmental factors. Discovering these genes is difficult, and in silico based strategies can significantly improve their detection. Data mining and automated tracking of new knowledge facilitate locus mapping. At the gene search stage, in silico prioritization of candidate genes plays an indispensable role in dealing with linked or associated loci. In silico analysis can also differentiate subtle consequences of coding DNA variants and remains the major method to predict functionality for non-coding DNA variants, particularly those in promoter regions. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539261 Fri, 21 Dec 2007 05:00:00 +0100 1539261 http://www.medworm.com/index.php?rid=1539260&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_7 In this study, we have used microarray technology to identify genes that are differentially regulated in response to activin-treated ovarian cancer cells. We find a number of biologically relevant genes that are involved in regulating activin signaling and genes potentially contributing to activin-mediated growth arrest appear to be differentially regulated. Thus, microarrays are an important tool for dissecting gene expression changes in normal physiological processes and disease. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539260 Fri, 21 Dec 2007 05:00:00 +0100 1539260 http://www.medworm.com/index.php?rid=1539259&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_4 Complex diseases and traits are influenced by a combination of genetic and environmental risk factors, some of which may be known, and many of which are unknown. It is possible to estimate the relative importance of the influence of genes and environment on a trait by studying correlations in the trait in related individuals. Known risk factors can be measured and included in the statistical models to understand disease etiology better. The joint effect of specific genes and environmental exposures can be estimated by measuring these in individuals, not necessarily related, with and without the disease of interest or with a range of trait values. These methods are illustrated by considering two example analyses in detail. The first is an analysis of a study of adolescent twins, quantifying... Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539259 Fri, 21 Dec 2007 05:00:00 +0100 1539259 http://www.medworm.com/index.php?rid=1539258&cid=s_37118_79_f&fid=37118&url=http%3A%2F%2Fwww.springerprotocols.com%2FAbstract%2Fdoi%2F10.1007%2F978-1-60327-148-6_17 In the post-Human Genome Project era, awareness of the resources available through the internet is essential to both molecular biologists and clinicians. An overview of the main databases and analytical tools described in this chapter is important to understand the principles upon which hypotheses are generated, experiments are based and conclusions reached. Similarly, an introduction to the terminology of these resources often facilitates their use and adoption into practice. This chapter covers database resources such as NCBI/ Entrez, Ensembl and UCSC as well as analytical tools for sequence alignment, promoter analysis and molecular interactions. (Source: Springer protocols feed by Bioinformatics) Springer protocols feed by Bioinformatics info http://www.medworm.com/rss/comments.php?id=1539258 Fri, 21 Dec 2007 05:00:00 +0100 1539258