GPI modification site prediction
The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.
Palmitoylation will enhance the surface hydrophobicity and membrane affinity of protein substrates, and play important roles in modulating proteins' trafficking and stability. After manual collection of the experimentally verified palmitoylation sites from scientific literature, we could get training data containing 439 palmitoylation sites from 194 distinct proteins, used to train the CSS-Palm program.
Neural network predictions for GlcNAc
O-glycosylation sites in Dictyostelium discoideum proteins.
EasyProt is a platform for mass spectrometry data processing, protein identification, quantification and unexpected PTM characterization. It provides a graphical interface to perform a large part of the proteomic data analysis workflow. Protein identification is based on OLAV scoring schemes and protein quantification is implemented (isobaric labeling and label-free). Features: peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging.
Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest.
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.
Calculate the mass of an oligosaccharide structure.
Predict 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.
, mass spectrometry (MS, MS/MS, LC-MS)
, molecular weight (MW)
, oligosaccharide (glycan, sugar)
, peptide mass fingerprinting
, post-translational modification (PTM)
, sequence analysis
, sugar epitope
GlycoSiteAlign selectively aligns amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.
Identification of GPI-anchor signals by a Kohonen self organizing map
Computational prediction of phosphorylation sites with their cognate protein kinases (PKs) is greatly helpful for further experimental design. GPS could predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy.
InsPecT is an MS/MS database search tool, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, InsPecT implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.
The LipoP 1.0 server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and N-terminal membrane helices in Gram-negative bacteria, with a good performance on sequences from Gram-positive bacteria also.
Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. Mascot integrates all of the proven methods of searching: Peptide Mass Fingerprint (the only experimental data are peptide mass values), Sequence Query (peptide mass data are combined with amino acid sequence and composition information), MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides.
MitoProt calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site.
Predict N-terminal myristoylation of proteins by neural networks. Myristoylator uses ensembles of neural networks, in order to learn to discriminate positive and negative sequences for N-myristoylation.
MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.
NetAcet predicts substrates of N-acetyltransferase A (NatA). The method was trained on yeast data but it obtains similar performance values on mammalian substrates acetylated by NatA orthologs.
Neural network predictions of C-mannosylation sites in mammalian proteins.