Table 1 Overview of Protein Bioinformatics Databases

Category	DB Short Name	DB Name	Database Content	URLs	Ref.
Sequence databases	CCDS	The Consensus CDS protein set database	Protein-coding regions that are identically annotated on the human and mouse reference genome assemblies	http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi	(1)
	DDBJ	DNA Data Bank of Japan	Annotated nucleotide sequence	http://www.ddbj.nig.ac.jp/	(2)
	ENA	European Nucleotide Archive	Raw sequencing data, sequence assembly information and functional annotation	http://www.ebi.ac.uk/ena	(3)
	GenBank	GenBank nucleotide sequence database	All publicly available DNA sequences	http://www.ncbi.nlm.nih.gov/genbank/	(4)
	RefSeq*	NCBI Reference Sequence Database	Comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins	http://www.ncbi.nlm.nih.gov/refseq/	(5)
	UniGene	Database of computationally identifies transcripts from the same locus	Gene-oriented nucleotide sequence clusters	http://www.ncbi.nlm.nih.gov/unigene/	(4)
	UniProtKB*	Universal Protein Resource (UniProt)	Comprehensive resource for protein sequence and annotation data	http://www.uniprot.org/	(6)
2D gel databases	COMPLUYEAST-2DPAGE	2-DE database at Universidad Complutense de Madrid, Spain	Candida albicans two-dimensional polyacrilamide gel electrophoresis database	http://compluyeast2dpage.dacya.ucm.es/	(7)
	REPRODUCTION-2DPAGE	2-DE database at Nanjing Medical University, China	Two-dimensional polyacrylamide gel electrophoresis database	http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi	(8)
	SWISS-2DPAGE	2-DE database at Swiss Institute of Bioinformatics, Switzerland	Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps	http://world-2dpage.expasy.org/swiss-2dpage/	(9)
	World-2DPAGE*	The World-2DPAGE database	2D-PAGE resources and tools	http://world-2dpage.expasy.org/repository/	(10)
3D structure databases	DisProt	Database of Protein Disorder	Information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part	http://www.disprot.org/	(11)
	MobiDB	Database of intrinsically disordered and mobile proteins	Intrinsically disordered and mobile proteins	http://mobidb.bio.unipd.it/	(12)
	ModBase	Database of Comparative Protein Structure Models	Annotated protein structure models	http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi	(13)
	PDBe*	Protein Data Bank at Europe	European resource for the collection, organization and dissemination of data on biological macromolecular structures	http://www.ebi.ac.uk/pdbe/	(14)
	PDBj*	Protein Data Bank at Japan	Centralized PDB archive of macromolecular structures and provides integrated tools	http://pdbj.org/	(15)
	PDBsum	Pictorial database of 3D structures in the Protein Data Bank	At-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB)	http://www.ebi.ac.uk/pdbsum/	(16)
	ProteinModelPortal	Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase	PSI-Nature Structural Biology Knowledgebase	http://www.proteinmodelportal.org/	(17)
	RCSB-PDB*	Protein Data Bank at RCSB	Single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids	http://www.pdb.org/	(18)
	SMR	Database of annotated 3D protein structure models	Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL	http://swissmodel.expasy.org/repository/	(19)
Chemistry databases	BindingDB	The Binding Datbase	Measured binding affinities data for protein targets and small molecules	http://www.bindingdb.org/	(20)
	ChEMBL*	Database of bioactive drug-like small molecules	Bioactive drug-like small molecules	https://www.ebi.ac.uk/chembldb	(21)
	DrugBank	Drug and Drug Target Databse	Detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information	http://www.drugbank.ca/	(22)
Enzyme and pathway databases	MetaCyc/BioCyc*	MetaCyc Database of Metabolic Pathways, BioCyc Collection of Pathway/Genome Databases	Full genome and predicted metabolic network of organism-specific Pathway/Genome Databases	http://www.biocyc.org/	(23)
	BRENDA*	BRaunschweig ENzyme DAtabase	Enzyme and enzyme-ligand information obtained from different sources	http://www.brenda-enzymes.org	(24)
	ENZYME	Enzyme nomenclature database	Information relative to the nomenclature of enzymes	http://enzyme.expasy.org/	(25)
	Reactome*	A knowledgebase of biological pathways and processes	Manually curated and peer-reviewed pathway database	http://www.reactome.org/	(26)
	SABIO-RK	SABIO-RK: Biochemical Reaction Kinetics Database	Biochemical reactions, their kinetic rate equations with parameters and experimental conditions	http://sabiork.h-its.org/	(27)
	SignaLink	A signaling pathway resource with multi-layered regulatory networks	Integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes	http://signalink.org/	(28)
	UniPathway	UniPathway: a resource for the exploration of metabolic pathways	Curated resource of enzyme-catalyzed and spontaneous chemical reactions	http://www.unipathway.org	(29)
Family and domain databases	Gene3D	Structural and Functional Annotation of Protein Families	Structural and Functional Annotation of Protein Families	http://gene3d.biochem.ucl.ac.uk/Gene3D/	(30)
	HAMAP	High-quality Automated and Manual Annotation of Proteins	Collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members	http://hamap.expasy.org/	(31)
	InterPro*	Integrated resource of protein families, domains and functional sites	Functional analysis of proteins by classifying them into families and predicting domains and important sites	http://www.ebi.ac.uk/interpro/	(32)
	PANTHER	The PANTHER Classification System	Classify proteins (and their genes) in order to facilitate high-throughput analysis	http://www.pantherdb.org/	(33)
	Pfam*	The Pfam protein families database	Protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)	http://pfam.xfam.org/	(34)
	PIRSF*	A whole-protein classification database	Whole-protein classification database	http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml	(35)
	PRINTS	Protein Motif fingerprint database	Protein fingerprints	http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/	(36)
	ProDom	Protein domain families database	Protein domain families automatically generated from the UniProt Knowledge Database	http://prodom.prabi.fr/prodom/current/html/home.php	(37)
	PROSITE*	Database of protein domains, families and functional sites	Protein domains, families and functional sites as well as associated patterns and profiles to identify them	http://prosite.expasy.org/	(38)
	ProtoNet	Automatic hierarchical classification of proteins	Automatic hierarchical classification of protein sequences	http://www.protonet.cs.huji.ac.il/	(39)
	SMART	Simple Modular Architecture Research Tool	Identification and annotation of genetically mobile domains and the analysis of domain architectures	http://smart.embl.de/	(40)
	SUPFAM	Superfamily database of structural and functional annotation	Structural and functional annotation for all proteins and genomes	http://supfam.org	(41)
	TIGRFAMs	TIGRFAMs protein family database	Curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins	http://www.jcvi.org/cgi-bin/tigrfams/index.cgi	(42)
Gene expression databases	Bgee	Database for Gene Expression Evolution	Comparison of expression patterns between animals	http://bgee.unil.ch	(43)
	CleanEx	Database of gene expression profiles	Gene expression data via unique approved gene symbols	http://cleanex.vital-it.ch/	(44)
	Genevisible	Search portal to normalized and curated expression data from Genevestigator	Curated expression data	http://genevisible.com/search	(45)
	ExpressionAtlas*	Database of Differential and Baseline Expression	Gene expression patterns under different biological conditions	http://www.ebi.ac.uk/gxa/home	(46)
Genome annotation databases	Ensembl*	Ensembl Eukaryotic genome annotation database	Annotations, querying tools and access methods for chordates and key model organisms	http://www.ensembl.org/	(47)
	EnsemblBacteria	Ensembl Bacteria genome annotation database	Genome sequences from bacteria and archaea have been annotated and deposited in the public archives of the members of the International Nucleotide Sequence Database Collaboration	http://bacteria.ensembl.org/	(48)
	EnsemblFungi	Ensembl Fungi genome annotation database	All fungal genomes whose sequence and annotation has been completed and submitted to the International Nucleotide Sequence Database Collaboration	http://fungi.ensembl.org/	(48)
	EnsemblMetazoa	Ensembl Metazoa genome annotation database	Genome sequences and annotations of all Ensembl Metazoa species	http://metazoa.ensembl.org/	(48)
	EnsemblPlants	Ensembl Plants genome annotation database	Genome sequences and annotations of all Ensembl Plants species	http://plants.ensembl.org/	(48)
	EnsemblProtists	Ensembl Protists genome annotation database	Genome sequences and annotations of all Ensembl Protists species	http://protists.ensembl.org/	(48)
	Entrez Gene*	Database of Genes of Genomes in the Reference Sequence Collection	Known and predicted genes defined by nucleo- tide sequence or map position	http://www.ncbi.nlm.nih.gov/gene	(49)
	KEGG	Kyoto Encyclopedia of Genes and Genomes	Biological interpretation of genome sequences and other high-throughput data	http://www.genome.jp/kegg/	(50)
	PATRIC	Bacterial Bioinformatics Resource Center	Bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools	http://patricbrc.org/	(51)
	UCSC*	UCSC Genome Bioinformatics	Reference sequence and working draft assemblies for a large collection of genomes	http://genome.ucsc.edu	(52)
	VectorBase	Bioinformatics Resource for Invertebrate Vectors of Human Pathogens	Invertebrate Vectors of Human Pathogens	http://www.vectorbase.org/	(53)
	WBParaSite	WormBase ParaSite	Parasitic worm genomics	http://parasite.wormbase.org	(54)
Organism specific databases	ArachnoServer	ArachnoServer: Spider toxin database	Information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom	http://www.arachnoserver.org	(55)
	CGD	Candida Genome Database	Genomic sequence data and gene and protein information for Candida albicans and related species	http://www.candidagenome.org/	(56)
	ConoServer	ConoServer: Cone snail toxin database	Sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails	http://www.conoserver.org/	(57)
	CTD	Comparative Toxicogenomics Database	Genes and proteins responding to environmental toxic agents across diverse species	http://ctdbase.org/	(58)
	dictyBase	Central resource for Dictyostelid genomics	Model organism database for the social amoeba Dictyostelium discoideum	http://dictybase.org/	(59)
	EchoBASE	EchoBASE - an integrated post-genomic database for E. coli.	Information from post-genomic experiments using the model bacterium Escherichia coli K-12	http://www.york.ac.uk/res/thomas/	(60)
	EcoGene	Escherichia coli strain K12 genome database	Structural and functional annotation of Escherichia coli K-12	http://www.ecogene.org/	(61)
	euHCVdb	The European Hepatitis C Virus database	Collection of computer-annotated sequences based on Hepatitis C Virus reference genomes	https://euhcvdb.ibcp.fr/euHCVdb/	(62)
	EuPathDB	Eukaryotic Pathogen Database Resources	Eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma	http://eupathdb.org/eupathdb/	(63)
	FlyBase*	A Database of Drosophila Genes & Genomes	Drosophila Genes and Genomes	http://flybase.org/	(64)
	GenAtlas	A database on genes, functions and related diseases	Scientific and clinical digests on human genes and diseases	http://genatlas.medecine.univ-paris5.fr/	(65)
	GeneCards	The Human Gene Database	All annotated and predicted human genes	http://www.genecards.org/	(66)
	GenoList	Integrated Environment for the Analysis of Microbial Genomes	Genome data from bacterial species	http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList	(67)
	Gramene	A comparative resource for plants	Data resource for comparative functional genomics in crops and model plant species	http://www.gramene.org/	(68)
	H-InvDB	H-Invitational Database	Curated annotations of human genes and transcripts	http://www.h-invitational.jp/	(69)
	HGNC	HUGO Gene Nomenclature Committee Database	Unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes	http://www.genenames.org/	(70)
	HPA	The Human Protein Atlas	A large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data	http://www.proteinatlas.org/	(71)
	HUGE	A Database of Human Unidentified Gene-Encoded Large Proteins	Large human proteins of hitherto unidentified functions	http://www.kazusa.or.jp/huge/	(72)
	LegioList	Legionella pneumophila genome database	Genomic information from L. pneumophila	http://genolist.pasteur.fr/LegioList/	(73)
	Leproma	Mycobacterium leprae genome database	Broad view of the Mycobacterium leprae genome	http://mycobrowser.epfl.ch/leprosy.html	(74)
	MaizeGDB	Maize Genetics and genomics Database	Curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays	http://www.maizegdb.org/	(75)
	MGD*	Mouse Genome Database	Integrated genetic, genomic, and biological data for the laboratory mouse	http://www.informatics.jax.org/	(76)
	Micado	MICrobial Advanced Database Organization	Microbial genomes and functional analysis of Bacillus subtilis	http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi	(77)
	OMIM	Online Mendelian Inheritance in Man	An Online Catalog of Human Genes and Genetic Disorders	http://www.omim.org/	(78)
	neXtProt*	Exploring the universe of human proteins	Human protein knowledge platform	http://www.nextprot.org/	(79)
	Orphanet	The portal for rare diseases and orphan drugs	Information on rare diseases and orphan drugs	http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB	(80)
	PharmGKB	The Pharmacogenomics Knowledgebase	Curated knowledge about the impact of genetic variation on drug response for clinicians and researchers.	http://www.pharmgkb.org	(81)
	PomBase	The scientific resource for fission yeast	Fission yeast Schizosaccharomyces pombe	http://www.pombase.org/	(82)
	PseudoCAP	The Pseudomonas Genome Database	Internet-based and community-based genome annotation project for analysis of a genome of a free-living organism	http://www.pseudomonas.com/	(83)
	RGD	Rat Genome Database	Genetic, genomic, phenotype, and disease data generated from rat research	http://rgd.mcw.edu/	(84)
	Rouge	A Database of Rodent Unidentified Gene-Encoded Large Proteins	Information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs)	http://www.kazusa.or.jp/rouge/	(72)
	SGD	Saccharomyces Genome Database	Comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae	http://www.yeastgenome.org/	(85)
	TAIR	The Arabidopsis Information Resource	Genetic and molecular biology data for the model higher plant Arabidopsis thaliana	http://www.arabidopsis.org/	(86)
	TubercuList	Mycobacterium tuberculosis strain H37Rv genome database	Mycobacterium tuberculosis genome database	http://tuberculist.epfl.ch	(87)
	WormBase	C. elegans and related nematodes Genetics and Genomics Database	Model organism database for Caenorhabditis elegans and other related nematodes	http://www.wormbase.org/	(54)
	Xenbase	Xenopus laevis and tropicalis biology and genomics resource	Diverse and rich genomic, expression and functional data available from Xenopus research	http://www.xenbase.org/	(88)
	ZFIN	The Zebrafish Model Organism Database	Zebrafish Information Network genome database	http://zfin.org/	(89)
Phylogenomic databases	eggNOG	Database of orthologous groups and functional annotation	Non-supervised orthologous groups (NOGs) from complete genomes	http://eggnog.embl.de/	(90)
	HOGENOM	Database of Homologous Genes from Fully Sequenced Organisms	Complete Genome Homologous Genes Families	http://pbil.univ-lyon1.fr/databases/hogenom/home.php	(91)
	HOVERGEN	Homologous Vertebrate Genes Database	Homologous vertebrate genes, structured under ACNUC sequence database management system	http://pbil.univ-lyon1.fr/databases/hovergen.html	(92)
	InParanoid	Eukaryotic Ortholog Groups with inparalogs	Protein orthologs inferred by the InParanoid algorithm	http://inparanoid.sbc.su.se/	(93)
	KO	Kyoto Encyclopedia of Genes and Genomes Orthology	Manually defined ortholog groups (KO entries), which are categorized under the hierarchy of KEGG pathways and BRITE ontologies	http://www.genome.jp/kegg/	(94)
	OMA*	The OMA orthology database	Inference of orthologs among complete genomes	http://omabrowser.org/	(95)
	OrthoDB	Database of Orthologous Groups	Catalog of orthologous protein-coding genes	http://cegg.unige.ch/orthodb6	(96)
	PhylomeDB	Database for complete catalogs of gene phylogenies (phylomes)	Complete catalogs of gene phylogenies (phylomes)	http://phylomedb.org/	(97)
	TreeFam	Database of animal gene trees	Phylogenetic trees inferred from animal genomes	http://www.treefam.org	(98)
Polymorphism and mutation databases	BioMuta	Single-nucleotide variation and disease association database	Curated single-nucleotide variation (SNV) and disease association database where the variations are mapped to the genome/protein/gene	https://hive.biochemistry.gwu.edu/tools/biomuta/	(99)
	dbSNP*	Database of Short Genetic Variations	Simple genetic variations such as single-base nucleotide substitutions, small-scale multi-base deletions or insertions, and microsatellite repeats	http://www.ncbi.nlm.nih.gov/SNP/	(4)
	DMDM	Domain Mapping of Disease Mutations	Unique domain-level view where all human coding mutations are mapped on the protein domain	http://bioinf.umbc.edu/dmdm/	(100)
Protein-protein interaction databases	BioGRID	The Biological General Repository for Interaction Datasets	Genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans	http://thebiogrid.org	(101)
	DIP	Database of Interacting Proteins	Experimentally determined interactions between proteins	http://dip.doe-mbi.ucla.edu/	(102)
	IntAct*	IntAct Molecular Interaction Database	Open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions	http://www.ebi.ac.uk/intact/	(103)
	MINT	The Molecular INTeraction database	Experimentally verified protein-protein interactions mined from the scientific literature by expert curators	http://mint.bio.uniroma2.it/mint/	(104)
	STRING	Search Tool for the Retrieval of Interacting Genes/Proteins	Known and Predicted Protein-Protein Interactions	http://string-db.org	(105)
Proteomic databases	MaxQB	The MaxQuant DataBase	Large proteomics projects and allows joint analysis and comparison	http://maxqb.biochem.mpg.de/mxdb/	(106)
	PaxDb	Protein Abundance Across Organisms	Comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues	http://pax-db.org	(107)
	PeptideAtlas*	PeptideAtlas	Peptides identified in a large set of tandem mass spectrometry proteomics experiments	http://www.peptideatlas.org	(108)
	PRIDE*	PRoteomics IDEntifications database	Centralized, standards compliant, public data repository for proteomics data	http://www.ebi.ac.uk/pride	(109)
	ProMEX	Protein Mass spectra EXtraction	Tryptic peptide fragmentation mass spectra derived from plants.	http://promex.pph.univie.ac.at/promex/	(110)
PTM databases	DEPOD*	The Human DEPhOsphorylation Database	Human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved	http://www.koehnlab.de/depod/index.php	(111)
	iPTMnet*	Protein post-translational modifications (PTMs) in systems biology context	Protein phosphorylation information	http://research.bioinformatics.udel.edu/iptmnet/	(112)
	PhosPhAt*	The Arabidopsis Protein Phosphorylation Site Database	Information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups	http://phosphat.uni-hohenheim.de	(113)
	Phospho.ELM*	Database of S/T/Y phosphorylation sites	Experimentally verified phosphorylation sites in eukaryotic proteins	http://phospho.elm.eu.org	(114)
	PhosphoGrid*	Database of experimentally verified in vivo protein phosphorylation sites	Experimentally verified in vivo protein phosphorylation sites in the model eukaryotic organism Saccharomyces cerevisisae	http://www.phosphogrid.org	(115)
	PhosphoSitePlus*	Phosphorylation site database	Comprehensive information and tools for the study of protein post-translational modifications (PTMs)	http://www.phosphosite.org	(116)
	UniCarbKB*	Database of glycomics and glycobiology	Online information storage and search platform for glycomics and glycobiology research	http://www.unicarbkb.org/	(117)
Ontology	GO*	Gene Ontology	Consistent descriptions of gene products across databases	http://www.geneontology.org/	(118)
	PRO	Protein Ontology	Ontological representation of protein-related entities by explicitly defining them and showing the relationships between them	http://pir.georgetown.edu/pro/pro.shtml	(119)
Specialized protein databases	Allergome	Allergome: platform for allergen knowledge	Allergenic molecules and proteins reported as allergens	http://www.allergome.org/	(120)
	CAZy	Carbohydrate-Active enZYmes Database	Families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds	http://www.cazy.org/	(121)
	ESTHER	ESTerases and alpha/beta-Hydrolase Enzymes and Relatives database	Proteins or protein domains belonging to the superfamily of alpha/beta-hydrolases, exemplified by the cholinesterases	http://bioweb.ensam.inra.fr/ESTHER/general?what=index	(122)
	GPCRDB	Information system for G protein-coupled receptors (GPCRs)	Data on sequences, ligand binding constants and mutations on G protein-coupled receptors (GPCRs)	http://www.gpcr.org/7tm/	(123)
	IMGT	The International ImMunoGeneTics information system	Immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species	http://www.imgt.org/	(124)
	MEROPS*	MEROPS protease database	Peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them	http://merops.sanger.ac.uk/	(125)
	MoonProt	Moonlighting protein database	Information about the proteins that have been experimentally verified to be moonlighting proteins	http://www.moonlightingproteins.org/	(126)
	mycoCLAP	Characterized Lignocellulose-Active Proteins of Fungal Origin	Fungal and bacterial genes encoding lignocellulose-active proteins that have been biochemically characterized	https://mycoclap.fungalgenomics.ca/mycoCLAP/	(127)
	PeroxiBase	The peroxidases database	Enzymes able to catalyze reduction of hydrogen peroxide and oxidize various substrates	http://peroxibase.toulouse.inra.fr/	(128)
	REBASE	The Restriction Enzyme Database	Information about restriction enzymes and related proteins	http://rebase.neb.com/rebase/rebase.html	(129)
	TCDB	Transporter Classification Database	Functional and Phylogenetic Classification of Membrane Transport Proteins	http://www.tcdb.org/	(130)
Other (Miscellaneous) databases	ChiTaRS	Database of chimeric transcripts and RNA-seq data	Chimeric RNAs from humans, mice and fruit flies with confirmation from RNA-seq reads	http://chitars.bioinfo.cnio.es/	(131)
	EvolutionaryTrace	Database of relative evolutionary importance of amino acids within a protein sequence	Evolutionary Trace Analysis of a protein structure	http://mammoth.bcm.tmc.edu/ETserver.html	(132)
	GeneWiki*	Wiki portal for the annotation of gene and protein function	Applying community intelligence to the annotation of gene and protein function	http://en.wikipedia.org/wiki/Portal:Gene_Wiki	(133)
	GenomeRNAi	Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens	Phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens	http://genomernai.dkfz.de/GenomeRNAi/	(134)
	PMAP-CutDB	Proteolytic event database	Proteolytic pathways	http://www.proteolysis.org/	(135)
	SOURCE	The Stanford Online Universal Resource for Clones and ESTs	Encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports	http://smd.princeton.edu/cgi-bin/source/sourceSearch	(136)

* Covered in section 3 of the chapter.

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