ExPASy Proteomics tools

Below are links from ExPASy Proteomics tools

protein identification and characterization
Identification and characterization with peptide mass fingerprinting data
Aldente - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest. FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides) Mascot - Peptide mass fingerprint from Matrix Science Ltd., London PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK PFMUTS - Shows the possible single and double mutations of a peptide fragment from MALDI peptide mass fingerprinting ProFound - Search known protein sequences with peptide mass information from Rockefeller and NY Universities [or from Genomic Solutions] ProteinProspector - UCSF tools for peptide masses data (MS-Fit, MS-Pattern, MS-Digest, etc.)
Identification and characterization with MS/MS data
Popitam - Identification and characterization tool for peptides with unexpected modifications (e.g. post-translational modifications or mutations) by tandem mass spectrometry Phenyx - Protein and peptide identification/characterization from MS/MS data from GeneBio, Switzerland Mascot - Sequence query and MS/MS ion search from Matrix Science Ltd., London OMSSA - MS/MS peptide spectra identification by searching libraries of known protein sequences PepFrag - Search known protein sequences with peptide fragment mass information from Rockefeller and NY Universities [or from Genomic Solutions] ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.) SearchXLinks - Analysis of mass spectra of modified, cross-linked, and digested proteins whose amino acid sequence is known, from Caesar, Germany
Identification with pI, Mw and/or amino acid composition
AACompIdent - Identify a protein by its amino acid composition AACompSim - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries TagIdent - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw MultiIdent - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data
Other prediction tools
GlycanMass - Calculate the mass of an oligosaccharide structure PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence PeptideMass - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence IsotopIdent - Predicts the theoretical isotopic distribution of a peptide, protein, polynucleotide or chemical compound

Post-translational modification prediction
ChloroP - Prediction of chloroplast transit peptides LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria MITOPROT - Prediction of mitochondrial targeting sequences PATS - Prediction of apicoplast targeted sequences PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum Predotar - Prediction of mitochondrial and plastid targeting sequences PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins SignalP - Prediction of signal peptide cleavage sites NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins) NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins NetNGlyc - Prediction of N-glycosylation sites in human proteins DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences big-PI Predictor - GPI Modification Site Prediction DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site) GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map Myristoylator - Prediction of N-terminal myristoylation by neural networks NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins NMT - Prediction of N-terminal N-myristoylation PrePS - Prenylation Prediction Suite Sulfinator - Prediction of tyrosine sulfation sites SUMOplot - Prediction of SUMO protein attachment sites

Post-translational modification prediction

ChloroP - Prediction of chloroplast transit peptides
LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria
MITOPROT - Prediction of mitochondrial targeting sequences
PATS - Prediction of apicoplast targeted sequences
PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum
Predotar - Prediction of mitochondrial and plastid targeting sequences
PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins
SignalP - Prediction of signal peptide cleavage sites
NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins
NetNGlyc - Prediction of N-glycosylation sites in human proteins
DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences
big-PI Predictor - GPI Modification Site Prediction
DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site)
GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
Myristoylator - Prediction of N-terminal myristoylation by neural networks
NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
NMT - Prediction of N-terminal N-myristoylation
PrePS - Prenylation Prediction Suite
Sulfinator - Prediction of tyrosine sulfation sites
SUMOplot - Prediction of SUMO protein attachment sites

Biological text analysis
AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query Protein Annotator's Assistant - A software system which assists protein annotators in the task of assigning functions to newly sequenced proteins XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

Biological text analysis

AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
Protein Annotator's Assistant - A software system which assists protein annotators in the task of assigning functions to newly sequenced proteins
XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE