ExPASy  (Expert Protein Analysis System)

PIR (Protein Information Resource)

PROSITE PROSITE dictionary of protein sites and patterns

PRINTS Protein Motif fingerprint database

InterPro Integrated Resources of Proteins Domains and Functional Sites

DOMO - Protein domain database in France (Automatically generated)

BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server

BLOCKS Blocks database

ProDOM Protein domain database (Automatically generated)

PDB Protein Data Bank

SWISS-MODEL Automatically generated protein models db

MODBASE Db of comparative protein structure models

SCOP Structural classification of proteins

CATH  UCL BSM structural classification of proteins

3DCrunch a Very Large Scale Protein Modelling Project

VAST  NCBI's structure-structure similarity search service

SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules

WORLD-2DPAGE  The most comprehensive Index to 2-D PAGE databases and services

Protein Prospector  Proteomics tools for mining sequence databases  in conjunction with Mass Spectrometry experiments

PepSea  an advanced tool for protein database searching by mass spectrometric data, such as peptide mass maps or (partial) amino acid sequences. 

PeptIdent  allows the identification of proteins using pI, Mw and peptide mass fingerprinting data (on ExPASy)

FindPept identify peptides that result from unspecific cleavage of proteins from their experimental masses (on ExPASy)

Profound protein identification by comparison of a peptide map to NCBI's nr databases using a Bayesian algorithm

PepFrag  protein identification by comparison of the fragmentation pattern of proteolytic peptides to a database

Mascot a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases.

SEQUEST

DIP Database of Interacting Proteins