Protein Bioinformatics Databases and Resources
Methods in molecular biologyPublished 1 January 2017Open access
Chuming Chen, Hongzhan Huang, Cathy Wu
Citations218
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
A comprehensive review of major protein bioinformatics databases is presented, with categorization and description, to help researchers quickly find the appropriate protein-related informatics resources.
Abstract
Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.
Keywords
ChemistryBiochemistry, Genetics and Molecular Biology
Nature GeneticsGene Ontology: tool for the unification of biology
44,650 Citations2000Michael Ashburner, Catherine A. Ball +18 more
The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Nucleic Acids ResearchThe Protein Data Bank
39,839 Citations2000Helen M. Berman
The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource are described.
Nucleic Acids ResearchKEGG: Kyoto Encyclopedia of Genes and Genomes
32,426 Citations1999Hiroyuki Ogata, Susumu Goto +4 more
KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, as well as the LIGAND database for chemical compounds and enzymes.
Nucleic Acids ResearchThe Pfam Protein Families Database
14,211 Citations2002Alex Bateman
In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up and new search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Nucleic Acids ResearchSTRING v10: protein–protein interaction networks, integrated over the tree of life
11,077 Citations2014Damian Szklarczyk, Andrea Franceschini +12 more
H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Nucleic Acids ResearchDatabase resources of the National Center for Biotechnology Information: update
11,002 Citations2003David Wheeler
BioinformaticsInterProScan 5: genome-scale protein function classification
9,998 Citations2014Philip Jones, David Binns +15 more
A new Java-based architecture for the widely used protein function prediction software package InterProScan is described, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis.
Nucleic Acids ResearchKEGG as a reference resource for gene and protein annotation
7,858 Citations2015Minoru Kanehisa, Yoko Sato +3 more
The KEGG GENES database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes, and new automatic annotation servers, BlastKOalA and GhostKOALA, are made available utilizing the non-redundant pangenome data set generated from theGENES database.
Nature Reviews GeneticsSequencing technologies — the next generation
7,038 Citations2009Michael L. Metzker
A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal of the American Society for Mass SpectrometryAn approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
6,626 Citations1994Jimmy K. Eng, Ashley L. McCormack +1 more
The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
Nucleic Acids ResearchThe carbohydrate-active enzymes database (CAZy) in 2013
6,488 Citations2013Vincent Lombard, Hemalatha Golaconda Ramulu +3 more
The changes that have occurred in CAZy during the past 5 years are outlined and a novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes is presented.
Nucleic Acids ResearchPfam: the protein families database
6,374 Citations2013ROBERT FINN, Alex Bateman +11 more
Nucleic Acids ResearchThe Reactome pathway Knowledgebase
5,994 Citations2015Antonio Fabregat, Konstantinos Sidiropoulos +20 more
The Reactome Knowledgebase provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a single consistent data model.
Nucleic Acids ResearchSWISS-MODEL: an automated protein homology-modeling server
5,656 Citations2003Torsten Schwede
The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.
Nucleic Acids ResearchUniProt: a hub for protein information
5,289 Citations2014Tunca Doğan
An annotation score for all entries in UniProt is introduced to represent the relative amount of knowledge known about each protein to help identify which proteins are the best characterized and most informative for comparative analysis.
Nucleic Acids ResearchThe KEGG resource for deciphering the genome
5,261 Citations2003M. Kanehisa
A knowledge-based approach for network prediction is developed, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes.
Analytical ChemistryEmpirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search
4,990 Citations2002Andrew Keller, Alexey I. Nesvizhskii +2 more
A statistical model is presented to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST, demonstrating that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides.
Analytical ChemistryA Statistical Model for Identifying Proteins by Tandem Mass Spectrometry
4,969 Citations2003Alexey I. Nesvizhskii, Andrew Keller +2 more
A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample, and it is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications.
Nucleic Acids ResearchNCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
4,573 Citations2006Kim D. Pruitt, Tatiana Tatusova +1 more
The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
BMC BioinformaticsThe COG database: an updated version includes eukaryotes
4,514 Citations2003Roman L. Tatusov, Natalie D. Fedorova +15 more
A major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes is described and is expected to be a useful platform for functional annotation of newlysequenced genomes, including those of complex eukARYotes, and genome-wide evolutionary studies.
Nucleic Acids ResearchGene Ontology Consortium: going forward
3,669 Citations2014The Gene Ontology Consortium
Improvements and expansions to several branches of the Gene Ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community are described.
Nucleic Acids ResearchOnline Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
3,512 Citations2004Ada Hamosh
Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics.
Nucleic Acids ResearchThe MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
3,499 Citations2015Ron Caspi, Richard Billington +13 more
This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; and several new search capabilities.
Nucleic Acids ResearchPhosphoSitePlus, 2014: mutations, PTMs and recalibrations
3,452 Citations2014Peter Hornbeck, Bin Zhang +4 more
The ‘PTMVar’ dataset, an intersect of missense mutations and PTMs from PSP, identifies over 25 000 PTMVars (PTMs Impacted by Variants) that can rewire signaling pathways.
Nucleic Acids ResearchHuman Protein Reference Database--2009 update
3,239 Citations2008Thottethodi Subrahmanya Keshava Prasad, Renu Goel +28 more
A number of new features in HPRD, including PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest, and a protein distributed annotation system—Human Proteinpedia.
Nature Structural & Molecular BiologyAnnouncing the worldwide Protein Data Bank
3,168 Citations2003Helen M. Berman, Kim Henrick +1 more
The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.
BioinformaticsThe systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models
3,150 Citations2003Michael Hucka, Andrew Finney +41 more
This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Nature ProtocolsLarge-scale gene function analysis with the PANTHER classification system
2,597 Citations2013Huaiyu Mi, Anushya Muruganujan +2 more
This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system, and redesigned the website interface to improve both user experience and the system's analytical capability.
Nature ProtocolsIntegration of biological networks and gene expression data using Cytoscape
2,574 Citations2007Melissa Cline, Michael Smoot +30 more
This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Nucleic Acids ResearchThe Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
2,570 Citations2011Philippe Lamesch, Tanya Berardini +15 more
Recent developments include several new genome releases, progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.
Nucleic Acids ResearchThe Database of Interacting Proteins: 2004 update
2,298 Citations2003Łukasz Salwiński
This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.
Nucleic Acids ResearchInterPro: the integrative protein signature database
2,156 Citations2008Sarah Hunter, Rolf Apweiler +36 more
The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
Nucleic Acids ResearchEntrez Gene: gene-centered information at NCBI
2,152 Citations2010Donna Maglott, James Ostell +2 more
The content in Entrez Gene represents the integration of curation and automated processing from NCBI’s Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI.
BioinformaticsUniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
2,131 Citations2014Barış Ethem Süzek, Yuqi Wang +3 more
The results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation.
Nucleic Acids ResearchDrugBank 4.0: shedding new light on drug metabolism
2,064 Citations2013Vivian Law, Craig Knox +16 more
The latest update of DrugBank, DrugBank 4.0, has been further expanded to contain data on drug metabolism, absorption, distribution, metabolism, excretion and toxicity (ADMET) and other kinds of quantitative structure activity relationships (QSAR) information.
Nucleic Acids ResearchBindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
2,049 Citations2006Tianbo Liu, Yu‐Ting Lin +3 more
BindingDB is a publicly accessible database currently containing ∼20 000 experimentally determined binding affinities of protein–ligand complexes, for 110 protein targets including isoforms and mutational variants, and ∼11000 small molecule ligands.
Nucleic Acids ResearchThe SWISS-MODEL Repository and associated resources
2,030 Citations2008Florian Kiefer, Konstantin Arnold +3 more
The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant models organisms.
Nucleic Acids ResearchSaccharomyces Genome Database: the genomics resource of budding yeast
1,971 Citations2011J. Michael Cherry, Eurie L. Hong +20 more
Nucleic Acids ResearchThe Reactome pathway knowledgebase
1,957 Citations2013David Croft, Antonio Fabregat Mundo +21 more
The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness and the data model has been extended to support annotation of disease processes due to infectious agents and to mutation.
Nucleic Acids ResearchThe Proteomics Identifications (PRIDE) database and associated tools: status in 2013
1,942 Citations2012Juan Antonio Vizcaíno, Richard G. Côté +16 more
Up-to-date statistics in data content are provided, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications.
Nucleic Acids ResearchThe MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases
1,902 Citations2013Sandra Orchard, Mais Ammari +33 more
All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Nucleic Acids ResearchSMART: recent updates, new developments and status in 2015
1,758 Citations2014Ivica Letunić, Tobias Doerks +1 more
The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million and a new, vector-based display engine has been developed for protein schematics in SMART.
Nucleic Acids ResearchScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
1,742 Citations2006Edouard de Castro, Christian J A Sigrist +6 more
A new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences that makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues.
BioinformaticsUniRef: comprehensive and non-redundant UniProt reference clusters
1,692 Citations2007Barış Ethem Süzek, Hongzhan Huang +3 more
Nucleic Acids ResearchNew and continuing developments at PROSITE
1,640 Citations2012Christian J A Sigrist, Edouard de Castro +6 more
Recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery are described.
Molecular & Cellular ProteomicsA Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics
1,574 Citations2005Mathias Uhlén, Erik Björling +65 more
A new publicly available database containing, in the first version, ∼400,000 high resolution images corresponding to more than 700 antibodies toward human proteins, providing a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues.
Nucleic Acids ResearchMEROPS: the database of proteolytic enzymes, their substrates and inhibitors
1,561 Citations2011Neil D. Rawlings, A. John Barrett +1 more
The MEROPS database has been expanded to include proteolytic enzymes other than peptidases, and the inclusion of small-molecule inhibitors in the tables of peptidase–inhibitor interactions is included.
Nucleic Acids ResearchThe ChEMBL bioactivity database: an update
1,548 Citations2013A. Patrícia Bento, Anna Gaulton +12 more
More comprehensive tracking of compounds from research stages through clinical development to market is provided through the inclusion of data from United States Adopted Name applications and a new richer data model for representing drug targets has been developed.
Nucleic Acids ResearchBioMagResBank
1,457 Citations2007Eldon L. Ulrich, Hideo Akutsu +14 more
The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules.
Nucleic Acids ResearchPATRIC, the bacterial bioinformatics database and analysis resource
1,342 Citations2013Alice R. Wattam, David Abraham +26 more
The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) and describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
Nucleic Acids ResearchThe InterPro protein families database: the classification resource after 15 years
1,277 Citations2014Alex Mitchell, Hsin-Yu Chang +34 more
The new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined, and the challenges faced by the resource given the explosive growth in sequence data in recent years are discussed.
Nucleic Acids ResearchThe MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
1,210 Citations2013Ron Caspi, Tomer Altman +18 more
MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature, and is the largest curated collection of metabolic pathways currently available.
BMC GenomicsBioMart – biological queries made easy
1,174 Citations2009Damian Smedley, Syed Haider +5 more
All aspects of BioMart are described from a user's perspective and it is demonstrated how it can be used to solve real biological use cases such as SNP selection for candidate gene screening or annotation of microarray results.
Nucleic Acids ResearchThe worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
1,165 Citations2006Helen M. Berman, K. Henrick +2 more
The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive, a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques.
Nucleic Acids ResearchEnsembl 2015
1,165 Citations2014Fiona Cunningham, M Ridwan Amode +47 more
The Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets, and the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl.
Nucleic Acids ResearchThe ENZYME database in 2000
1,140 Citations2000Amos Bairoch
The ENZYME database is a repository of information related to the nomenclature of enzymes that became an indispensable resource for the development of metabolic databases in recent years.
Nucleic Acids ResearchThe EMBL Nucleotide Sequence Database
1,108 Citations2000William Baker
The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (EBI) is maintained at the European Bioinformatics Institute in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA).
Nucleic Acids ResearchModBase, a database of annotated comparative protein structure models, and associated resources
1,093 Citations2010Ursula Pieper, Benjamin Webb +15 more
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models that allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server.
Nucleic Acids ResearchGPCRdb: an information system for G protein-coupled receptors
1,090 Citations2015Vignir Ísberg, Stefan Mordalski +8 more
New features in the fifth major GPCRdb release are highlighted, including G PCR crystal structure browsing, superposition and display of ligand interactions, direct deposition by users of point mutations and their effects on ligand binding.
Nucleic Acids ResearchMINT, the molecular interaction database: 2012 update
1,057 Citations2011Luana Licata, Leonardo Briganti +10 more
The growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction are reported here.
Nucleic Acids ResearchCDD: specific functional annotation with the Conserved Domain Database
1,055 Citations2008Aron Marchler‐Bauer, James B. Anderson +26 more
NCBI's Conserved Domain Database is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution, and provides annotation of domain footprints and conserved functional sites on protein sequences.
ElectrophoresisProteome and proteomics: New technologies, new concepts, and new words
1,052 Citations1998N. Leigh Anderson, Norman G. Anderson +2 more
Quantitative analysis of protein expression data obtained by high‐throughput methods has led to define the concept of “regulatory homology” and use it to begin to elucidate the basic structure of gene expression control in vivo.
Nucleic Acids ResearchREBASE—a database for DNA restriction and modification: enzymes, genes and genomes
1,043 Citations2009Richard J. Roberts, Tamas Vincze +2 more
The fastest growing segment of REBASE contains the putative R–M systems found in the sequence databases, including summary schematics.
Nucleic Acids ResearchThe TIGRFAMs database of protein families
986 Citations2003Daniel H. Haft
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIG RFAMs, Pfam and InterPro models designed to support both automated and manually curated annotation of genomes.
CellCharacterization of the Yeast Transcriptome
970 Citations1997Victor E. Velculescu, Lin Zhang +7 more
The integration of positional information with gene expression data allowed for the generation of chromosomal expression maps identifying physical regions of transcriptional activity and identified genes that had not been predicted by sequence information alone.
Nucleic Acids ResearchSMART 6: recent updates and new developments
960 Citations2008Ivica Letunić, Tobias Doerks +1 more
The domain annotations were extended with data on metabolic pathways and links to several pathways resources, and the interaction network view was completely redesigned and is now available for more than 2 million proteins.
Nucleic Acids ResearchThe UCSC Genome Browser database: 2015 update
939 Citations2014Kate R. Rosenbloom, Joel Armstrong +27 more
A browser for the first new human genome reference assembly in 4 years in December 2013, a watershed comparative genomics annotation (100-species multiple alignment and conservation), and a novel distribution mechanism for the browser are among the highlights of the past year.
Briefings in BioinformaticsPROSITE: A documented database using patterns and profiles as motif descriptors
931 Citations2002Christian J A Sigrist
The close relationship of PROSite with the SWISS-PROT protein database allows the evaluation of the sensitivity and specificity of the PROSITE motifs and their periodic reviewing.
PLoS BiologyThe Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
925 Citations2007Shibu Yooseph, Granger Sutton +31 more
This work used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling sequences to add a great deal of diversity to known protein families and shed light on their evolution.
Nucleic Acids ResearchThe BioGRID interaction database: 2015 update
925 Citations2014Andrew Chatr‐aryamontri, Bobby‐Joe Breitkreutz +20 more
The BioGRID architecture has been improved to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.
HAL (Le Centre pour la Communication Scientifique Directe)The Universal Protein Resource (UniProt) in 2010
924 Citations2010Rolf Apweiler, M Caroline Martin +132 more
The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community.
Nucleic Acids ResearchReactome knowledgebase of human biological pathways and processes
886 Citations2008Lisa Matthews, Gopal Gopinath +18 more
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, Drosophila and Gallus gallus.
Nucleic Acids ResearchThe PeptideAtlas project
886 Citations2005Frank Desiere
A summary of the process and details about the Human, Drosophila and Yeast PeptideAtlas builds are presented and a uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications.
Nucleic Acids Research<i>MEROPS</i>: the database of proteolytic enzymes, their substrates and inhibitors
851 Citations2013Neil D. Rawlings, Matthew A. Waller +2 more
The MEROPS filing pipeline has been altered to circumvent the restrictions imposed on non-interactive blastp searches, and a HMMER search using specially generated alignments to maximize the distribution of organisms returned in the search results has been added.
Nucleic Acids ResearchThe BioMart community portal: an innovative alternative to large, centralized data repositories
840 Citations2015Damian Smedley, Syed Haider +103 more
The latest version of the BioMart Community Portal comes with many new databases that have been created by the ever-growing community and comes with better support and extensibility for data analysis and visualization tools.
Nucleic Acids ResearchDisProt: the Database of Disordered Proteins
806 Citations2006Megan D. Sickmeier, John A. Hamilton +10 more
The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs) by collecting and organizing knowledge regarding the experimental characterization and the functional associations of IDPs.
Journal of Biomedical InformaticsBio2RDF: Towards a mashup to build bioinformatics knowledge systems
798 Citations2008François Belleau, Marc-Alexandre Nolin +3 more
The present article details this new approach to build mashups of bioinformatics data and illustrates the building of a mashup used to explore the implication of four transcription factor genes in Parkinson's disease.
Nature BiotechnologyA common open representation of mass spectrometry data and its application to proteomics research
793 Citations2004Patrick G. A. Pedrioli, Jimmy K. Eng +23 more
The 'mzXML' format is introduced, an open, generic XML (extensible markup language) representation of MS data that will facilitate data management, interpretation and dissemination in proteomics research.
Nucleic Acids ResearchREBASE—a database for DNA restriction and modification: enzymes, genes and genomes
785 Citations2014Richard J. Roberts, Tamas Vincze +2 more
Genome ResearchJBrowse: A next-generation genome browser
776 Citations2009Mitchell E. Skinner, Andrew Uzilov +3 more
An open source, portable, JavaScript-based genome browser that can be used to navigate genome annotations over the web, and a simple wiki plug-in that allows users to upload and share annotation tracks is described.
Nucleic Acids ResearchPhospho.ELM: a database of phosphorylation sites--update 2011
766 Citations2010Holger Dinkel, Claudia Chica +5 more
Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score and the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation.
Nature BiotechnologyThe minimum information about a proteomics experiment (MIAPE)
752 Citations2007Chris Taylor, Norman W. Paton +27 more
The processes and principles underpinning the development of guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry are described and the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector are discussed.
Nucleic Acids ResearchArrayExpress update—simplifying data submissions
721 Citations2014N. N. Kolesnikov, Emma Hastings +16 more
The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold and will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines in the near future.
Briefings in BioinformaticsPathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
707 Citations2009Peter D. Karp, Suzanne Paley +12 more
An overview of Pathway Tools capabilities is provided, which performs multiple computational inferences including Prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons, and provides a large number of query and visualization tools.
Nucleic Acids ResearchThe BioGRID Interaction Database: 2008 update
699 Citations2007Bobby‐Joe Breitkreutz, C. Stark +10 more
A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations.
Nucleic Acids ResearcheggNOG v4.0: nested orthology inference across 3686 organisms
691 Citations2013Sean Powell, Kristoffer Forslund +11 more
The fourth version of the eggNOG database is presented, that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families.
Nucleic Acids ResearchThe IntAct molecular interaction database in 2010
629 Citations2009Bruno Aranda, Premanand Achuthan +19 more
In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data, which allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies.
Nucleic Acids ResearchThe ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
613 Citations2012Janna Hastings, Paula de Matos +9 more
This work has completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology, and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them.
PROTEOMICSVersion 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines
610 Citations2015Mingcong Wang, Christina Herrmann +3 more
It is reported that a significant fraction of published experiments cannot readily be accessed and/or parsed for quantitative information, requiring additional steps and efforts.
Nature MethodsProtein interaction data curation: the International Molecular Exchange (IMEx) consortium
574 Citations2012Sandra Orchard, Samuel Kerrien +29 more
The International Molecular Exchange consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website.
EMBO ReportsPeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
545 Citations2008Eric W. Deutsch, Henry Lam +1 more
The PeptideAtlas Project is described, its contents and components are described, and it is shown how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.
Nucleic Acids ResearchThe Transporter Classification Database
521 Citations2013Milton H. Saier, Vamsee Reddy +2 more
This manuscript describes an update of the database descriptions previously featured in NAR database issues, which are of increasing usefulness to the international scientific community and can serve as a model for the expansion of database technologies.
Nucleic Acids ResearchInParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
518 Citations2014Erik L. L. Sonnhammer, Gabriel Östlund
InParanoid release 8 is based on the 66 reference proteomes that the ‘Quest for Orthologs’ community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes—in total 273 species.
Nucleic Acids ResearchThe 20 years of PROSITE
502 Citations2007N. Hulo, Amos Bairoch +7 more
The implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSite methods are described.
Nucleic Acids ResearchSUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
497 Citations2008Derek A. Wilson, Ralph Pethica +6 more
SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt and recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles.
Nucleic Acids ResearchFlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
489 Citations2014Gilberto dos Santos, Andrew J. Schroeder +6 more
The attributes of the new Release 6 reference genome assembly are described, the migration of FlyBase genome annotations to this new assembly is described, how genome features on this newAssembly can be viewed in FlyBase and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.
TuberculosisThe MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes
484 Citations2010Adamandia Kapopoulou, J. Lew +1 more
An overview of the functionalities available and the different ways of interrogating the data is provided then how both the new information and the latest features are helping the mycobacterial research communities are discussed.
BrainProteome-based plasma biomarkers for Alzheimer's disease
474 Citations2006Abdul Hye, Steven Lynham +18 more
It is suggested that blood may be a rich source for biomarkers of Alzheimer's disease and that complement factor H, together with other proteins such as alpha-2M, May be a specific markers of this illness.
…