sib logo SIB resources
external logo External resources - (No support from the ExPASy Team)

Databases

  • UniProtKB/Swiss-Prot  •  UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB. It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis. [less]
  • SugarBind  •  This database provides a list of known carbohydrate sequences to which pathogenic organisms specifically adhere via lectins or adhesins. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.  [less]
  • UniCarbKB  •  UniCarbKB is a curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures. It includes data previously available from GlycoSuiteDB. [less]

Tools

  • big-PI  •  GPI modification site prediction  [less]
  • ChloroP  •  The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.  [less]
  • CSS-Palm  •  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. [less]
  • DAS-TMfilter  •  DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library. [less]
  • DictyOGlyc  •  Neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins. [less]
  • FindMod  •  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. [less]
  • GlycanMass  •  Calculate the mass of an oligosaccharide structure. [less]
  • GlycoMod  •  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. [less]
  • GPI-SOM  •  Identification of GPI-anchor signals by a Kohonen self organizing map [less]
  • GPS  •  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. [less]
  • HMMTOP  •  Prediction of transmembranes helices and topology of proteins. [less]
  • ISMARA  •  MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets. [less]
  • LipoP  •  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. [less]
  • MITOPROT  •  MitoProt calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site. [less]
  • Myristoylator  •  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. [less]
  • NetAcet  •  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.  [less]
  • NetCGlyc  •  Neural network predictions of C-mannosylation sites in mammalian proteins.  [less]
  • NetCorona  •  NetCorona predicts coronavirus 3C-like proteinase (or protease) cleavage sites using artificial neural networks on amino acid sequences. Every potential site is scored and a list is compiled in addition to a graphical representation. [less]
  • NetGlycate  •  Predicts glycation of epsilon amino groups of lysines in mammalian proteins.  [less]
  • NetNES  •  NetNES 1.1 server predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins using a combination of neural networks and hidden Markov models.  [less]
  • NetNGlyc  •  NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.  [less]
  • NetOGlyc  •  Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. [less]
  • NetPhos  •  NetPhos produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.  [less]
  • NetPhosK  •  The NetPhosK 1.0 server produces neural network predictions of kinase specific eukaryotic protein phosphorylation sites. Currently NetPhosK covers the following kinases: PKA, PKC, PKG, CKII, Cdc2, CaM-II, ATM, DNA PK, Cdk5, p38 MAPK, GSK3, CKI, PKB, RSK, INSR, EGFR and Src.  [less]
  • NetPhosYeast  •  predict serine and threonine phosphorylation sites in yeast proteins [less]
  • NetPicoRNA  •  The NetPicoRNA 1.0 server produces neural network predictions of cleavage sites of picornaviral proteases. [less]
  • NMT  •  Prediction of N-terminal N-myristoylation of proteins [less]
  • Phobius  •  Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. [less]
  • PredictProtein  •  PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges. [less]
  • Predotar  •  Predotar was designed for systematic screening of large batches of proteins for identifying putative targeting sequences, and recognizes the N-terminal targeting sequences of classically targeted precursor proteins. It provides a probability estimate as to whether the sequence contains a mitochondrial, plastid or ER targeting sequence. [less]
  • PrePS  •  The prenylation prediction suite (PrePS) combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each of the prenyltransferases.  [less]
  • ProP  •  ProP 1.0 server predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase (PC) prediction.  [less]
  • PTS1  •  predict peroxisomal targeting signal 1 containing proteins [less]
  • QuickMod  •  QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.  [less]
  • SecretomeP  •  The SecretomeP 2.0 server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.  [less]
  • SignalP  •  SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. [less]
  • SOSUI  •  Classification and Secondary Structure Prediction of Membrane Proteins. [less]
  • Sulfinator  •  The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well as sulfated tyrosines clustered within 25 amino acid windows, respectively. All four HMMs contain the distilled information from one multiple sequence alignment. [less]
  • SUMOplot  •  The SUMOplot??? Analysis Program predicts and scores sumoylation sites in your protein. The presence of this post-translational modification may help explain larger MWs than expected on SDS gels due to attachment of SUMO protein (11kDa) at multiple positions in your protein. [less]
  • SUMOsp  •  Protein sumoylation plays important roles in a variety of biological processes, such as transcriptional regulation, signaling transduction, cell cycle progression and differentiation. SUMOsp predicts sumoylation sites in proteins. [less]
  • TargetP  •  TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).  [less]
  • TatP  •  TatP 1.0 server predicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of two artificial neural networks. A postfiltering of the output based on regular expressions is possible.  [less]
  • TermiNator  •  TermiNator predicts N-terminal methionine excision, N-terminal acetylation, N-terminal myristoylation and S-palmitoylation of either prokaryotic or eukaryotic proteins originating from organellar or nuclear genomes. It also relates the predicted N-terminus to protein half-life (5-220 hours) and relative translation efficiency (relative value 1-5) of eukaryotic proteins. [less]
  • TMHMM  •  TMHMM is a membrane protein topology prediction method based on a hidden Markov model (HMM). It predicts transmembrane helices in proteins. [less]
  • YinOYang  •  The YinOYang WWW server produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify "Yin-Yang" sites.  [less]