Peptide mass fingerprinting (Matrix Science Ltd., London)
ProFound
Peptide mass fingerprinting (The Rockefeller
University)
ProteinProspector
MS-Fit, MS-Tag, MS-Digest, MS-Seq and
more (UCSF)
PeptideCutter
Predicts cleavage sites in a given protein
generated by proteases or chemicals (ExPASy)
PeptIdent
This tool utilizes
pI, MW and peptide mass fingerprinting data to identify proteins (ExPASy)
TagIdent
Proteins can be matched based on a short sequence tag of up
to 6 amino acids against proteins in the SWISS-PROT/TrEMBL databases close
to a given pI and MW (ExPASy )
Compute pI/MW
This tool calculates the
theoretical pI (isoelectric point) and MW (molecular weight) for a list
of SWISS-PROT and/or TrEMBL entries, or for a user entered sequence (ExPASy)
MW, pI, Titration Curve
This tool calculates the theoretical pI and
MW, and a titration curve (L'Atelier BioInformatique de Marseille)
Translate
Translates a nucleotide (DNA/RNA) sequence to a protein sequence (ExPASy
)
NCBI BLAST
A tool that allows protein and nucleotide BLAST (Basic
Local Alignment Search Tool) (NCBI)
BLink
A systematic and automatic
link to the BLAST search result (NCBI)
Scansite
This tool searches
for possible phosphorylation motifs within proteins, or sites that bind
to domains such as SH2 domains, 14-3-3 domains or PDZ domains (MIT)
Motif Scan
Scans for all known motifs that occur in a sequence (SIB )
InterProScan
one of the tools used for searching protein function based
on integrated search (EBI)
FindMod
a tool that can predict potential
protein post-translational modifications (Pé) from known Pés in the database
and find potential single amino acid substitutions in peptides (ExPASy
)
GlycoMod
a tool that can predict the possible oligosaccharide structures
that occur on proteins from their experimentally determined masses. The
program can be used for free or derivatized oligosaccharides and for glycopeptides
( ExPASy )
NetPhos
The NetPhos WWW server produces neural network predictions
for serine, threonine and tyrosine phosphorylation sites in eukaryotic
proteins (CBS)
Kyte-Doolittle Hydropathy Plots
A tool to plot the hydropathicity
of protein from individual hydropathic index of amino acid residues. (Positive
values represent hydrophobicity and negative values represent hydrophilicity)
(FASTA)
épred
The épred program makes a prediction of membrane-spanning
regions and their orientation. The algorithm is based on the statistical
analysis of ébase, a database of naturally occurring transmembrane proteins.
The prediction is made using a combination of several weight-matrices
for scoring (EMBnet.org)
Membrane Protein Explorer
A tool for exploring
the topology and other features of membrane proteins by means of hydropathy
plots, using thermodynamic principles (Stephen White, UC Irvine)
TargetP
Prediction of subcellular location (CBS)
TMAP
Transmembrane prediction
based on multiple sequence alignment (Karolinska Institutet) Note:These
proteomics tools are accessed on-line at no charge. Please inform us of
other search tools or software that is valuable to you in your research.
You can e-mail us directly at:proteomics@UCDHSC.edu.
