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Protein Information

Entrez Proteins - 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.

PROW - Protein Resources on the Web - short authoritative guides on the approximately 200 human CD cell-surface molecules. Peer-reviewed; provides approximately 20 standardized categories of information (biochemical function, ligands, etc.) for each CD antigen.

Protein Sequence Analysis - various tools are available for analyzing protein sequences

Protein Data Bank - t he single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

CluSTr Offers an automatic classification of UniProt/Swiss-Prot + UniProt/TrEMBL.

CSA *** CSA - The Catalytic Site Atlas is a resource of catalytic sites and residues identified in enzymes using structural data.

GO *** The EBI's Gene Ontology consortium pages. GO is an international consortium of scientists with the editorial office based at the EBI.

GOA *** Provides assignments of gene products to the Gene Ontology (GO) resource.

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.

Proteome Analysis
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/UniRef *** A non-redundant archive of protein sequences extracted from public databases and contains only protein sequences.

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)

Additional on-line resources – other databases for protein interactions and protein structure

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