These sites guide you to the protein databases available for proteomics and some of the bioinformatics software available for accessing these databases.The "What can Proteomics Software do?" page of this site also lists a number of these database resources.

Protein and Gene Databases

Each year the journal Nucleic Acids Research (NAR) publishes an issue devoted to the databases of genes and proteins. Databases of special note are SWISS-PROT, IPI, PIR and NCBI. UniProt is “the world’s most comprehensive catalog of information about proteins”. The Bioinformatic Harvester combines the protein and gene information from 15 databases.

Proteomic and Genomic Web Services

Nucleic Acids Research also publishes an issue on web servers listing web tools that you can use such as BLAST, ESLpred, SDPpred, iMolTalk, ProMoST, and many, many others.

bioinformatics.net

Bioinformatics.net lists resources for bioinformatics and molecular biology including proteomics. It has links to protein and peptide databases as well as software and tutorials. This site is also known as www.molbiol.net.

Ionsource provides a similar service for mass spec information.

Peptide Atlas

Peptide atlas is a collection of MS/MS data that has been analyzed for peptide identification. The Open Proteomics Database, the Sashimi data repository, and Quartz also have proteomics mass spec data. The Global Proteome Machine (GPM) organization has a database for storing the results of searches by X!Tandem. The World 2D PAGE site lists 2D gels for many tissue samples.

Protein mods - RESID

RESID provides a comprehensive collection of the types of modifications possible for proteins. UniMod, Delta Mass are other lists of post translational modifications. FindMod is a tool for searching for modifications.

Human Proteomics Initiative

This site's goal is to annotate all the known human proteins. This annotation will include function, domain structure, subcellular location, post-translational modifications, variants, and similarities to other proteins. The status as of Jan 2005 was about 12,000 human proteins annotated with 5,000 splice variants, 20,000 mutations and polymorphisms and 30,000 modifications.

Human Genome Variation Society

This site is your guide to dozens of databases that deal with mutations, polymorphisms, alleles, and SNPs. Some of these databases are oriented to specific human disorders.

The Alternative Splicing Gallery shows how each gene is assembled into multiple proteins by splice variants.

Human Protein Reference Database

This site has integrated info on domains, post translational modifications, interaction networks and disease associations for each protein in the human proteome.

ELM - Functional sites

ELM predicts functional sites in eukaryotic proteins. This site has links to dozens of other sites that examine protein motifs and domains.

The Codon Usage Database tells the codon frequency in hundreds of species.

Match Miner

It is very annoying that the same gene will have different names or ID's in different databases. MatchMiner translates between a number of these database identifiers as does DAVID and Onto-express. The HUGO gene nomenclature site lists the "official" names for genes.