Protein databases

Secondary and tertiary structures of proteins

• PDB - Protein data bank
• PDBsum
• The Swiss-3DImage Collection of proteins
• HSSP,FSSP,DSSP - structure-sequence alignments of proteins
• BLOCK - protein classification based on multiple alignments of conserved regions
• SBASE - protein domain library
• PRINTS - protein fingerprint database
• PROSITE - significant patterns and profiles in proteins
• PIR - the Protein Information Resource
• DOCK - docking of molecules
• Cambridge Crystallographic Data Centre
• NMR links at Oxford
• BioMagResBank - Data from NMR
• SCOP - Structural Classification of Proteins
• CATH - Structural Classification of Proteins
• FSSP - Structural Classification of Proteins
• TOPS - Protein Topology
• ProDom - Protein Domain databese
• PAPIA - Parallel Protein Information Analysis system
• GPCRDB - Information system for G protein-coupled receptors
• NIH Molecular Modeling
• Amber
• RasMol
• MolScript
• QUEST 2D gel protein database
• 2-DE Protein Database
• 2DE maps (LSD)
• Protein Structure Initiative (PSI)

Protein sequences

• SWISS-PROT, SWISS-2DPAGE and SWISS-MODEL databases
• PIR - Protein Sequence Database
• GRBase - proteins involved in gene regulation
• TRANSFAC - transcription factors and their DNA binding sites
• Histone sequence database
• G-protein-coupled Receptor Database
• MHCPEP - database of MHC-binding peptides (gopher)
• O-GLYCBASE - database of O-glycosylated proteins

Protein Structure Prediction

• CASP - prediction center
• Modeller-homology modeling
• PHD-secondary structure
• PREDATOR-secondary structure
• Threader-threading
• 123D-threading
• SOSUI-Prediction of Transmembrane Segments
• HMMTOP

Enzyme, metabolic pathway, antigen databases

• ENZYME nomenclature database
• REBASE - restriction enzymes and methylases
• EMP - Enzymes and Metabolic Pathways database
• Hybridoma Data Bank - search for a mAb against a specific antigen
• Enzyme structure database based on PDB
• Ribonuclease P database
• EcoCyc - Encyclopedia of E. coli genes and metabolism
• GenProtEc - Escherichia coli genes and their gene products
• EC-Enzyme - an enzyme classification database