Bioinformatics Links Directory : Proteomics

This section contains links to general proteomics resources, methods, software, and databases.

DeNovoID - (Found July 2, 2008 )

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.
http://proteomics.mcw.edu/denovoid/

PROWL - (Found July 2, 2008 )

Software tools and integrated databases to facilitate analyzing the output from protein mass spectrometry experiments.
http://prowl.rockefeller.edu/

ProteomicsSURF - (Found July 2, 2008 )

ProteomicsSURF is a site dedicated to disease proteomics which aims to identify proteins involved in human disease and to understand how their expression, structure and function cause illness.
http://www.proteomicssurf.com/

Proteome Analyst - (Found July 2, 2008 )

Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.
http://www.cs.ualberta.ca/~bioinfo/PA/

Proteome Analysis at EBI - (Found July 2, 2008 )

The Proteome Analysis Database at EBI provides statistical and comparative analyses of the predicted proteomes of organisms for which there are fully-sequenced genomes.
http://www.ebi.ac.uk/proteome/

Proteios - The Open Source Proteomics Initiative - (Found July 2, 2008 )

Proteios is an initiative to create an open-source storage, analysis and organization system for proteomics experiments.
http://www.proteios.org/

ProteinProspector - (Found July 2, 2008 )

Various tools used for sequence database mining in connection with mass spectrometry experiments.
http://prospector.ucsf.edu/

PeptIdent - (Found July 2, 2008 )

PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data.
http://us.expasy.org/tools/peptident.html

PEDRo - (Found July 2, 2008 )

Software and schemata for modelling, capturing and disseminating proteomics experimental data
http://pedrodownload.man.ac.uk/

Neuropred - (Found July 2, 2008 )

NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.
http://neuroproteomics.scs.uiuc.edu/neuropred.html