IMPORTANT:

Please note that this page is not updated anymore and remains static.
However, many of the external resources listed below are available in the category proteomics on the portal.

[Protein identification and characterization] [Other proteomics tools] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Sequence alignment] [Phylogenetic analysis] [Biological text analysis][Statistics]
Protein identification and characterization
Identification and characterization with peptide mass fingerprinting data
  • FindMod SIB logo - 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 SIB logo - 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
  • Mascot - Peptide mass fingerprint from Matrix Science Ltd., London
  • PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK
  • 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
  • QuickMod SIB logo - Open modification spectral library search tool for identification of MS/MS data
  • Phenyx genebio logo - 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
  • ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)
Identification with isoelectric point, molecular weight and/or amino acid composition
  • AACompIdent SIB logo - Identify a protein by its amino acid composition
  • AACompSim SIB logo - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries
  • TagIdent SIB logo - Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw
  • MultiIdent SIB logo - Identify proteins with isoelectric point (pI), molecular weight (Mw), amino acid composition, sequence tag and peptide mass fingerprinting data
Other prediction or characterization tools
  • ProtParam SIB logo - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
  • Compute pI/Mw SIB logo - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
  • PeptideCutter SIB logo - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
  • PeptideMass SIB logo - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence
  • xComb - computes all possible crosslinks based on proteins of interest for further interrogation using standard search engine
  • xQuest - Search machine to identify cross-linked peptides from complex samples and large protein sequence databases
  • SmileMS genebio logo - Small molecule identification
  • SmileMS molecule toolkit genebio logo SIB logo - isotopes pattern calculator, mass to formula, mass to pubchem compounds
Other proteomics tools
Glycotools
  • GlycanMass SIB logo - Calculate the mass of an oligosaccharide structure
  • GlycoMod SIB logo - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)
  • GlycospectrumScan - an analytical tool independent of MS-platform that accurately identifies and assigns the oligosaccharide heterogeneity on glycopeptides from MS data of a mixture of peptides and glycopeptides (Reference)
  • Glycoviewer - a visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG) (Reference)
Other tools for MS data (vizualisation, quantitation, analysis, etc.)
  • HCD/CID spectra merger SIB logo - a tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines
  • MALDIPepQuant SIB logo - Quantify MALDI peptides (SILAC) from Phenyx output
  • MSight SIB logo - Mass Spectrometry Imager
  • pIcarver SIB logo - Visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies
Other tools for 2-DE data (image analysis, data publishing, etc.)

DNA -> Protein

Similarity searches
  • BLAST SIB logo Network Service on ExPASy
  • BLAST SIB logo at EMBnet-CH/SIB (Switzerland)
  • BLAST at NCBI
  • WU-BLAST at Bork's group in EMBL (Heidelberg)
  • WU-BLAST and BLAST at the EBI (Hinxton)
  • BLAST at PBIL (Lyon)
  • Fasta3 - FASTA version 3 at the EBI
  • MPsrch - Smith/Waterman sequence comparison at EBI
  • PropSearch - Structural homolog search using a 'properties' approach at Montpellier
  • SAMBA - Systolic Accelerator for Molecular Biological Applications
  • SAWTED - Structure Assignment With Text Description
  • Scanps - Similarity searches using Barton's algorithm
  • SEQUEROME - BLAST similarity search and sequence profiling at Georgetown University
  • SHOPS - Analysis of the genomic operon context for any group of proteins
  • BLAST2FASTA - Converts NCBI BLAST output into FASTA format

Pattern and profile searches
  • InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
  • MyHits SIB logo - Relationships between protein sequences and motifs
  • ScanProsite SIB logo - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
  • HamapScan SIB logo - Scans a sequence against the HAMAP families
  • MotifScan SIB logo - Scans a sequence against protein profile databases (including PROSITE)
  • Pfam HMM search - Scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre]
  • ProDom - Compares sequences with ProDom search utility
  • SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
  • FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
  • 3of5 - Complex Pattern Search - e.g. to search for a motif with 3 basic AA in 5 positions
  • ELM - Eukaryotic Linear Motif resource for functional sites in proteins
  • PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy SIB logo]
  • PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
  • PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL
  • PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL
  • SMART - Simple Modular Architecture Research Tool; at EMBL
  • TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM
  • 9aaTAD - Prediction of Nine Amino Acid Transactivation Domain

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
  • DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
  • NetCGlyc - C-mannosylation sites in mammalian proteins
  • NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins
  • NetGlycate - Glycation of epsilon amino groups of lysines in mammalian proteins
  • NetNGlyc - Prediction of N-glycosylation sites in human proteins
  • OGPET - Prediction of O-GalNAc (mucin-type) glycosylation sites in eukaryotic (non-protozoan) proteins
  • YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences
  • big-PI Predictor - GPI Modification Site Prediction
  • GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
  • Myristoylator SIB logo - Prediction of N-terminal myristoylation by neural networks
  • NMT - Prediction of N-terminal N-myristoylation
  • CSS-Palm - Palmitoylation site prediction with CSS
  • PrePS - Prenylation Prediction Suite
  • NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
  • NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
  • NetPhosK - Kinase specific phosphorylation sites in eukaryotic proteins
  • NetPhosYeast - Serine and threonine phosphorylation sites in yeast proteins
  • GPS - Prediction of kinase-specific phosphorylation sites for 408 human protein kinases in hierarchy
  • Sulfinator SIB logo - Prediction of tyrosine sulfation sites
  • SulfoSite - Prediction of tyrosine sulfation sites
  • SUMOplot - Prediction of SUMO protein attachment sites
  • SUMOsp - Prediction of sumoylation sites
  • TermiNator - Prediction of N-terminal modification (version 3)
  • NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
  • NetCorona - Coronavirus 3C-like proteinase cleavage sites in proteins
  • ProP - Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences

Topology prediction
  • NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins
  • PSORT - Prediction of protein subcellular localization
  • SecretomeP - Non-classical and leaderless secretion of proteins
  • TargetP - Prediction of subcellular location
  • TatP - Twin-arginine signal peptides
  • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)
  • HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)
  • PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)
  • SOSUI - Prediction of transmembrane regions (Nagoya University, Japan)
  • TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
  • TMpred SIB logo - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
  • TopPred - Topology prediction of membrane proteins (France)

Primary structure analysis
  • ProtParam SIB logo - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
  • Compute pI/Mw SIB logo - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
  • ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states
  • MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve
  • Scratch Protein Predictor
  • HeliQuest - A web server to screen sequences with specific alpha-helical properties
  • Radar - De novo repeat detection in protein sequences
  • REP - Searches a protein sequence for repeats
  • REPRO - De novo repeat detection in protein sequences
  • T-REKS - De novo detection and alignment of repeats in protein sequences
  • TRUST - De novo repeat detection in protein sequences
  • XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences
  • SAPS SIB logo - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]
  • Coils SIB logo - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]
  • Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
  • Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilities with the Paircoil algorithm.
  • Multicoil - Prediction of two- and three-stranded coiled coils
  • 2ZIP - Prediction of Leucine Zippers
  • ePESTfind - Identification of PEST regions
  • HLA_Bind - Prediction of MHC type I (HLA) peptide binding
  • PEPVAC - Prediction of supertypic MHC binders
  • RANKPEP - Prediction of peptide MHC binding
  • SYFPEITHI - Prediction of MHC type I and II peptide binding
  • ProtScale SIB logo - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
  • Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
  • Peptide Builder
  • Protein Colourer - Tool for coloring your amino acid sequence
  • Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa
  • Three-/one-letter amino acid converter - Tool which converts amino acid codes from three-letter to one-letter and vice versa.
  • Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
  • PepDraw - peptide primary structure drawing
  • RandSeq SIB logo - Random protein sequence generator

Secondary structure prediction
  • AGADIR - An algorithm to predict the helical content of peptides
  • APSSP - Advanced Protein Secondary Structure Prediction Server
  • CFSSP - Chou & Fasman Secondary Structure Prediction Server
  • GOR - Garnier et al, 1996
  • HNN - Hierarchical Neural Network method (Guermeur, 1997)
  • HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction
  • Jpred - A consensus method for protein secondary structure prediction at University of Dundee
  • JUFO - Protein secondary structure prediction from sequence (neural network)
  • NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions
  • NetTurnP - Prediction of Beta-turn regions in protein sequences
  • nnPredict - University of California at San Francisco (UCSF)
  • Porter - University College Dublin
  • PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University
  • Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction
  • PSA - BioMolecular Engineering Research Center (BMERC) / Boston
  • PSIpred - Various protein structure prediction methods at Bloomsbury Centre for Bioinformatics
  • SOPMA - Geourjon and Delage, 1995
  • Scratch Protein Predictor
  • DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology

Tertiary structure
Tertiary structure analysis
  • iMolTalk - An Interactive Protein Structure Analysis Server (currently down)
  • MolTalk - A computational environment for structural bioinformatics
  • COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities
  • PoPMuSiC - Prediction of thermodynamic stability changes upon point mutations; design of modified proteins
  • Seq2Struct - A web resource for the identification of sequence-structure links
  • STRAP - A structural alignment program for proteins
  • TLSMD - TLS (Translation/Libration/Screw) Motion Determination
  • TopMatch-web - Protein structure comparison
Tertiary structure prediction
Homology modeling
  • SWISS-MODEL SIB logo - An automated knowledge-based protein modelling server
  • CPHmodels - Automated neural-network based protein modelling server
  • ESyPred3D - Automated homology modeling program using neural networks
  • Geno3d - Automatic modelling of protein three-dimensional structure
Threading
  • Phyre (Successor of 3D-PSSM) - Automated 3D model building using profile-profile matching and secondary structure
  • Fugue - Sequence-structure homology recognition
  • HHpred - Protein homology detection and structure prediction by HMM-HMM comparison
  • LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
  • SAM-T08 - HMM-based Protein Structure Prediction
  • PSIpred - Various protein structure prediction methods (including threading) at Bloomsbury Centre for Bioinformatics
Ab initio
Assessing tertiary structure prediction
  • Anolea - Atomic Non-Local Environment Assessment
  • LiveBench - Continuous Benchmarking of Structure Prediction Servers
  • NQ-Flipper - Validation and correction of asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography
  • PROCHECK - Verification of the stereochemical quality of a protein structure
  • ProSA-web - Recognition of errors in 3D structures of proteins
  • QMEAN SIB logo - Server for Model Quality Estimation
  • What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics
Quaternary structure
  • MakeMultimer - Reconstruction of multimeric molecules present in crystals
  • EBI PISA - Protein Interfaces, Surfaces and Assemblies
  • PQS - Protein Quaternary Structure Query form at the EBI
  • ProtBud - Comparison of asymmetric units and biological units from PDB and PQS
Molecular modeling and visualization tools
Prediction of disordered regions

Sequence alignment
Binary
  • LALIGN SIB logo - Finds multiple matching subsegments in two sequences
  • Dotlet SIB logo - A Java applet for sequence comparisons using the dot matrix method
Multiple
Alignment analysis
  • AMAS - Analyse Multiply Aligned Sequences
  • Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).
  • CINEMA - Color Interactive Editor for multiple alignments
  • ESPript - Tool to print a multiple alignment
  • MaxAlign - Post-processing of alignments by removing sequences (taxa) with many gaps
  • PhyloGibbs SIB logo - Gibbs motif sampler incorporating phylogeny and tracking statistics
  • SVA - Sequence Variability Analyser for multiple alignments
  • PVS - A protein variability server optimized for conserved epitope discovery
  • WebLogo - Sequence logos at Berkeley/USA
  • plogo - Sequence logos at CBS/Denmark
  • GENIO/logo - Sequence logos at Stuttgart/Germany
  • SeqLogo - Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)

Phylogenetic analysis

Biological text analysis
  • AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
  • BioMinT - Mining the biomedical literature
  • GPSDB SIB logo - Gene and Protein Synonym DataBase
  • Medline Ranker
  • The Miner Suite - of bioinformatic software packages and data analysis
  • XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

Statistical tools
  • pROC SIB logo - A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves)

Last modified 27/Sep/2010 by GRR