AACompSim is a tool which allows the comparison of the amino acid composition of a Swiss-Prot entry with all other Swiss-Prot entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry. ExPASY. - [Read more AACompSim tool]
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. ExPASy - [Read more Aldente]
CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns. - [Read more CysView]
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. ExPASy - [Read more FindMod]
Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM), protease autolytic cleavage. ExPASy - [Read more FindPept]
The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes. - [Read more GDAP]
Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides). ExPASy - [Read more GlycoMod]
LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constraints may also be specified, inc - [Read more LINKER]
Peptide Mass. Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence. ExPASY. - [Read more Peptide Mass]
Peptide cutter. Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence. ExPASY. - [Read more Peptidecutter]
Pro Found is Proteometrics search engine for obtaining protein sequences that best match a list of peptide masses. It uses a well-tested Bayesian algorithm to identify proteins based on many criteria, such as: - [Read more ProFound.]
Protein Info is Proteometrics search engine obtaining protein sequences that match a particular sequence motif. Fragments of sequence information can be entered and all of the sequences matching that pattern in a particular database are retrieved. Protein - [Read more ProteinInfo]
Protein Prospector. A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with mass spectrometry experiments. - [Read more ProteinProspector]
Compute molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. - [Read more ProtParam]
Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins. - [Read more Qgrid]
Sonar MS/MS Search Engine is Proteometrics search engine for identifying proteins using MS/MS information from digest peptides. It has been designed specifically for the needs of protein identification automation, using breakthrough concepts and designs t - [Read more Sonar MS/MS Search Engine.]
Includes chemical structures and properties, solvent accessibility, post-translational modifications, and more; with references. - [Read more The Amino Acid Repository]
