protein databases
- 1. Protein Sequence databases 1. UniProt Universal Protein Resource (UniProt Consortium: EBI, Expasy, PIR) 2. PIR Protein Information Resource (Georgetown University Medical Center (GUMC)) 3. Swiss-Prot Protein Knowledgebase (Swiss Institute of Bioinformatics) 4. PEDANT Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit) 5. PROSITE Database of Protein Families and Domains 6. DIP Database of Interacting Proteins (Univ. of California) 7. Pfam Protein families database of alignments and HMMs (Sanger Institute) 8. PRINTS PRINTS is a compendium of protein fingerprints (Manchester University) 9. ProDom Comprehensive set of Protein Domain Families (INRA/CNRS) 10. SignalP 3.0 Server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs 11. SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms 12. Annotation Clearing House a project from the National Microbial Pathogen Data Resource 13. InterPro Classifies proteins into families and predicts the presence of domains and sites. Proteomics databases 1. Proteomics Identifications Database (PRIDE) A public repository for proteomics data, containing protein and peptide identifications and their associated supporting evidence as well as details of post- translational modifications. (European Bioinformatics Institute) Protein structure databases Protein Data Bank (PDB) comprising:  Protein DataBank in Europe (PDBe)  ProteinDatabank in Japan (PDBj)  Research Collaboratory for Structural Bioinformatics (RCSB)
- 2. Secondary databases 1. SCOP Structural Classification of Proteins 2. CATH Protein Structure Classification 3. PDBsum Protein model databases 1. SWISS-MODEL Server and Repository for Protein Structure Models 2. ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF) 3. Protein Model Portal (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland) Protein-protein interactions 1. BIND Biomolecular Interaction Network Database 2. BioGRID A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute) 3. CCSB Interactome 4. DIP Database of Interacting Proteins 5. IntAct molecular interaction database: a central, standards-compliant repository of molecular interactions, including protein–protein, protein–small molecule and protein–nucleic acid interactions. 6. NetPro 7. STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL)