Revised May 2013
- NCBI Protein - search protein sequence records (from GenPept + RefSeq + Swiss-Prot + PIR + RPF + PDB) by accession number, author name, organism, gene/protein name, and a variety of other text terms
- RefSeq - NCBI database of Reference Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, mRNAs and proteins for gene models, and entire chromosomes.
- FTP GenPept - download the "genpept.fsa.Z" file, which contains FASTA formatted amino acid translations extracted from GenBank/EMBL/DDBJ records that are annotated with one or more CDS features
- Conserved Domain Database (CDD) - a collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. It includes domains from Smart and Pfam, as well as domains contributed by NCBI researchers.
- Protein Data Bank - the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
- CSA *** CSA - The Catalytic Site Atlas is a resource of catalytic sites and residues identified in enzymes using structural data.
- HPI Human Proteomics Initiative (HPI) is an initiative, by SIB and the EBI, to annotate all known human sequences according to the quality standards of UniProt/Swiss-Prot.
- IntAct *** IntAct is a protein interaction database and analysis system. It provides a query interface and modules to analyse interaction data.
- IntEnz *** The Integrated relational Enzyme database (IntEnz) will contain enzyme data approved by the Nomenclature Committee. The goal is to create a single relational enzyme database.
- InterPro *** The InterPro database is an integrated documentation resource for protein families, domains and functional sites.
- IPI - International Protein Index a non-redundant human proteome set constructed from UniProt/Swiss-Prot, UniProt/TrEMBL, Ensembl and RefSeq.
- PANDIT *** PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees. PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
- Ensembl Genomes - Statistical and comparative analysis of the predicted proteomes of fully sequenced organisms.
- UniProt/Knowledgebase *** A centralised resource for protein sequences and is the central hub for the collection of functional information on proteins, with accurate, consistent, and rich annotation, the amino acid sequence, protein name or description, taxonomic data and citation information.
- UniProt/UniParc *** Features clustering of similar sequences to yield a representative subset of sequences. This produces very fast search times.
- UniProt/Swiss-Prot - An annotated protein sequence database. Part of the UniProt Knowledgebase.
- UniProt/TrEMBL - A computer generated protein database enriched with automated classification and annotation. Part of the UniProt Knowledgebase.
- ExPASY Molecular Biology Server - is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
- Molecular Model Database – NCBI molecular structure database
- Conserved Domain Database
- Membrane Protein resources
- Vector Alignment Search Tool (VAST) - is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user.
- 3D Structure Viewer Freeware (Cn3D) - Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
- Database of Quantitative Cellular Signaling (DOQCS) - is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.
- Cytoscape - A bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
- Kyoto Encyclopedia of genes and genomes (pathways)
- National Center for Macromolecular Imaging (NCMI)
- BioPathways Consortium
- NIGMS Protein Structure Initiative
- NIGMS Program Announcement Structural Biology of Membrane Proteins
- BISTI
- HUPO Proteomics Standards Initiative
- Membrane Protein Production for Structure Determination (R01)
- HUPO Human Brain Protein Project
- Harvard University Institute of Proteomics
- NIGMS Glue grant: "Lipids Map"
- Consortium for Functional Glycomics
- DOE -- Oakridge National Laboratory
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