http://precedings.nature.com/tags/protein Recently posted documents tagged with 'protein' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3287.1 The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC). These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse reference genomes, and consistently updated by collaborating members (CCDS). NCBI curation of any one data type (e.g., a gene) is closely integrated with evaluation of the genome assembly, and determining annotation by way of RefSeq transcript and protein sequences. Database and work-flow infrastructure is designed to support reporting and tracking issues with the assembly, gene, or evidence data to collaborating groups, and to support collaborative review and discussions of issues that arise. Curation depends on publicly available information to represent the gene extent, alternatively spliced transcripts, and protein isoforms. Scientific consults occur regularly and wet-bench validation needs are supported by some of the collaborations. Curation of genome annotation results in improved data presentation at the three major genome browser sites (Ensembl, NCBI, UCSC) and has resulted in efforts to define common curation guidelines to maximize consistency and minimize conflicts.The presentation focuses on curation of the human genome, genes, and RefSeq sequence standards. http://dx.doi.org/10.1038/npre.2009.3287.1 Wed, 27 May 2009 22:41:09 UTC Curation at the NCBI: Genomes, Genes, & Sequence Standards doi:10.1038/npre.2009.3287.1 2009-05-27 Kim D. Pruitt Nature Precedings 2009-05-27T22:41:09Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3200.1 Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets.Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome’s data content and software can all be freely used and redistributed under open source terms. Reactome instances are cross-referenced to corresponding ones in databases including EntrezGene, OMIM, Ensembl, UniProt, the UCSC Genome Browser, KEGG, ChEBI, and Gene Ontology. http://dx.doi.org/10.1038/npre.2009.3200.1 Sun, 03 May 2009 15:44:21 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2009.3200.1 2009-05-07 Bijay Jassal Nature Precedings 2009-05-03T15:44:21Z Poster Chemistry Genetics & Genomics Immunology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3152.1 Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction.The Eukaryotic Linear Motif resource (ELM – http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc.In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain. By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process. http://dx.doi.org/10.1038/npre.2009.3152.1 Thu, 23 Apr 2009 17:20:38 UTC The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins doi:10.1038/npre.2009.3152.1 2009-04-23 Francesca Diella Nature Precedings 2009-04-23T17:20:38Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3157.1 The nematode worm, Caenorhabditis elegans, was the first multicellular organism to be sequenced. Its genome was published in 1998, providing an impetus for gene and protein annotation. Recently, the genome of C. briggsae has been sequenced. This has given bioinformaticans the opportunity to study comparative genomics between two highly similar organisms. Currently, there are 12 species of Caenorhabditis in UniProtKB and over 700 nematode species, including some of interest to parasitology. Functional and sequence annotation from literature and sequence analysis tools are included in each curated record. C. elegans has a relatively small genome size, short life span and a transparent body, making it ideal for knock-out/RNAi studies. Thus many C. elegans UniProtKB entries have characterization details in the newly introduced DISRUPTION PHENOTYPE comment. Many more worm genome sequencing projects are underway, three of which involve species from the Caenorhabditis genus (C. brenneri, C. japonica and C.remanei). We look forward to working with this influx of data and continuing our close collaboration with WormBase. http://dx.doi.org/10.1038/npre.2009.3157.1 Thu, 23 Apr 2009 17:20:07 UTC Worm Annotation in the UniProt Knowledgebase (UniProtKB) doi:10.1038/npre.2009.3157.1 2009-04-23 Duncan J. Legge Nature Precedings 2009-04-23T17:20:07Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3153.1 The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence annotation from the literature and sequence analysis tools, using both controlled vocabularies (including GO terms) and free text. The tetraploid nature of the X. laevis and D. rerio genomes complicates annotation since the protein copies need to be identified and curated as separate UniProtKB/Swiss-Prot entries. The recent addition of Xenbase cross-references in Xenopus UniProtKB entries has been the result of cross-talk with Xenbase, and we continue to collaborate with ZFIN to ensure consistency between databases. UniProt is mainly supported by the NIH, European Commission FELICS, Swiss Federal Government, PATRIC BRC and NSF grants. http://dx.doi.org/10.1038/npre.2009.3153.1 Thu, 23 Apr 2009 17:20:01 UTC Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB) doi:10.1038/npre.2009.3153.1 2009-04-23 Rebecca E. Foulger Nature Precedings 2009-04-23T17:20:01Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3120.1 Most sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool SPIN. Curators use a range of sequence analysis tools to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be kept confidential for a limited period at the submitter’s request. UniProtKB submission is complemented by the journal scan project that monitors the scientific literature for papers containing directly sequenced proteins. UniProtKB entries are then created for those sequences that are not yet in the database and have not been submitted via SPIN. http://dx.doi.org/10.1038/npre.2009.3120.1 Wed, 22 Apr 2009 16:48:09 UTC Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal Scanning doi:10.1038/npre.2009.3120.1 2009-04-22 Paul Browne Nature Precedings 2009-04-22T16:48:09Z Poster Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3129.1 UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system and plans for its future development and enhancement will be presented. http://dx.doi.org/10.1038/npre.2009.3129.1 Wed, 22 Apr 2009 13:12:51 UTC Evidence attribution in the UniProt Knowledgebase doi:10.1038/npre.2009.3129.1 2009-04-22 Michele Magrane Nature Precedings 2009-04-22T13:12:51Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3108.1 Background – The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.Results – In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for Chlamydomonas reinhardtii (ChlamyCyc) was established, which currently features about 270 metabolic pathways with related genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.Conclusion – Chlamycyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas reinhardtii. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de. http://dx.doi.org/10.1038/npre.2009.3108.1 Tue, 21 Apr 2009 17:08:33 UTC ChlamyCyc – a comprehensive database and web-portal centered on Chlamydomonas reinhardtii doi:10.1038/npre.2009.3108.1 2009-04-21 Jan-Ole Christian Nature Precedings 2009-04-21T17:08:33Z Poster Genetics & Genomics Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/826/version/1 Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin. http://precedings.nature.com/documents/826/version/1 Mon, 27 Aug 2007 09:46:57 UTC Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks hdl:10101/npre.2007.826.1 2007-08-27 Markus J. Buehler Nature Precedings 2007-08-27T09:46:57Z Manuscript Biotechnology Chemistry Ecology Molecular Cell Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.50.1 Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications. http://dx.doi.org/10.1038/npre.2007.50.1 Thu, 14 Jun 2007 13:14:29 UTC Fast and Scriptable Molecular Graphics in Web Browsers without Java3D doi:10.1038/npre.2007.50.1 2007-06-14 Egon Willighagen Nature Precedings 2007-06-14T13:14:29Z Manuscript Chemistry Bioinformatics http://creativecommons.org/licenses/by/2.5/