- DIP Database of Interacting Proteins
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
 http://dip.doe-mbi.ucla.edu
- Database Collection @HUPO
A comprehensive list of proteomics specific databases compiled by HUPO
http://www.hupo.org/link/databases.htm
- ExPASy Molecular Biology Server
Proteomics server of the Swiss Institute of Bioinformatics. Includes tools for analysis of protein sequences and structures as well as 2-D PAGE.
http://www.expasy.org/
- Expression proteomics
Bio-Rad's approach to expression proteomics focuses on three technologies: sample preparation, 2-D electrophoresis, and imaging and analysis.
http://www.proteomeworkssystem.com/
- FishProm at the University of Aberdeen
Protocols and research into salmonid fish, rainbow trout liver proteins, their expression, biochemical pathways and degradation, using mass spectrometry and 2-dimensional electrophoresis.
http://www.abdn.ac.uk/fishprom/index.shtml
- Human Protein Reference Database
The HPRD represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
- Human Proteomics Initiative
Project to annotate all known human sequences according to the quality standards of SWISS-PROT
http://www.expasy.ch/sprot/hpi/
- NCI-Proteomics Program
With combined force of biomedical and clinical proteomics, NCI-Proteomics Program sets its quest to identify and characterize the protein signatures of human cancer cells and tissues and to apply proteomics technologies directly to patient diagnosis, toxicity monitoring, and therapeutic intervention.
http://web.ncifcrf.gov/rtp/prot/site/default_flash.asp
- NCT Proteomics Group
The mission of this program is to identify key proteins and pathways involved in the response to environmental toxicants and stressors.
http://dir.niehs.nih.gov/proteomics/home.htm
- NHLBI Proteomics Initiatives
The NHLBI funded 10 highly interactive, multi-disciplinary Proteomic Centers to enhance and develop innovative proteomic technologies and apply them to relevant biological questions that will advance our knowledge of heart, lung, blood, and sleep health and disease.
http://www.nhlbi.nih.gov/resources/medres/proteomics/index.htm
- OPD: Open Proteomics Database
OPD is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains ~400,000 spectra representing experiments from 4 different organisms.
http://bioinformatics.icmb.utexas.edu/OPD/
- PROWL
Resource for protein chemistry and mass spectrometry protocols, including synthetic analogues and surfactant anomolies, maintained at the Rockefeller University, NY.
http://prowl.rockefeller.edu/
- Plasma Proteome Institute
PPI is working to define the research and regulatory agenda required to rapidly advance the exploration and diagnostic use of the human plasma proteome.
http://www.plasmaproteome.org/
- ProteinProspector
Resource for mining sequence databases in conjunction with mass spectrometry experiments, maintained by Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA.
http://prospector.ucsf.edu/
- Proteome Database of Lactococcus lactis
With extensible protein attributes in database scheme and a clear graphical user interface, the proteomic database offers a dynamic online access with web-enabled frontends. Database of 2D Reference Maps (IPG-Dalt) and summarized protein information, such as Mr, pI, CAI and GRAVY.
http://www.wzw.tum.de/proteomik/lactis/
- SWICZ: Swiss-Czech Proteomics Server
Presents database and experimental procedures for two bacterial species, Caulobacter crescentus and Streptomyces coelicolor. Joint venture between Prague and Basel, Switzerland.
http://proteom.biomed.cas.cz/
- Scansite
Protein substrate site search and prediction tool. Includes other utilities, such as a molecular weight and isoelectric point calculator.
http://scansite.mit.edu/
- Swedish Human Proteome Resource
A program devoted to systematic generation of antibodies to a non-redundant set of human proteins, and to use these reagents for functional exploration of protein variants and interactions.
http://www.biotech.kth.se/molbio/hpr/
- UniProt: the Universal Protein Resource
UniProt is the world's most comprehensive catalog of information on proteins with a central database of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.ebi.uniprot.org/index.shtml
- proteomicsSURF
The public resource for clinical proteomics and proteomic technologies
http://proteomicssurf.com/
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