ExPASy Proteomics tools

ExPASy Proteomics tools: The tools marked by are local to the ExPASy server. The remaining tools are developed and hosted on other servers.

ExPASy Proteomics tools

Protein identification and characterization

Identification and characterization with peptide mass fingerprinting data

• 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. Download the stand-alone version
• FindMod - 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 - 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
• GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)
• 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.)

ExPASy Proteomics tools

Identification and characterization with MS/MS data

• Popitam - Identification and characterization tool for peptides with unexpected modifications (e.g. post-translational modifications or mutations) by tandem mass spectrometry
• Phenyx - 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 [or from Genomic Solutions]
• ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)
• xQuest - search machine to identify cross-linked peptides from complex samples and large protein sequence databases

Identification with isoelectric point, molecular weight and/or amino acid composition

• AACompIdent - Identify a protein by its amino acid composition
• AACompSim - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries
• TagIdent - 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 - 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 - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
• Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
• GlycanMass - Calculate the mass of an oligosaccharide structure
• PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
• PeptideMass - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence
• IsotopIdent - Predicts the theoretical isotopic distribution of a peptide, protein, polynucleotide or chemical compound

Other proteomics tools

Other tools for MS data (vizualisation, quantitation, analysis, etc.)

• MALDIPepQuant - Quantify MALDI peptides (SILAC) from Phenyx output
• MSight - Mass Spectrometry Imager
• pIcarver - 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.)

• ImageMaster / Melanie - Software for 2-D PAGE analysis
• Make2D-DB II - A package to build a web-based proteomics database

ExPASy Proteomics tools

DNA -> Protein

• Translate - Translates a nucleotide sequence to a protein sequence
• Transeq - Nucleotide to protein translation from the EMBOSS package
• Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner
• BCM search launcher - Six frame translation of nucleotide sequence(s)
• Reverse Translate - Translates a protein sequence back to a nucleotide sequence
• (Reverse)-Transcription and Translation Tool
• Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
• LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters
• List of gene identification software sites

Similarity searches

• BLAST Network Service on ExPASy
• BLAST 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
• FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH
• 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

Pattern and profile searches

• InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
• Hits - Relationships between protein sequences and motifs
• ScanProsite - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
• HamapScan - Scans a sequence against the HAMAP families
• MotifScan - 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]
• FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
• 3of5 - Complex Pattern Search
• ELM - Eukaryotic Linear Motif resource for functional sites in proteins
• PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ]
• 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

ExPASy Proteomics tools

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
• DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site)
• GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
• Myristoylator - 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 - 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)
• TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
• TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
• TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
• TopPred - Topology prediction of membrane proteins (France)

ExPASy Proteomics tools

Primary structure analysis

• ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
• Compute pI/Mw - 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
• Radar - De novo repeat detection in protein sequences
• REP - Searches a protein sequence for repeats
• REPRO - De novo repeat detection in protein sequences
• TRUST - De novo repeat detection in protein sequences
• XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences
• SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]
• Coils - 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 probabilitis with the Paircoil algorithm.
• Multicoil - Prediction of two- and three-stranded coiled coils
• 2ZIP - Prediction of Leucine Zippers
• PESTfind - Identification of PEST regions at EMBnet Austria
• 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 - 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
• HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel
• RandSeq - Random protein sequence generator

Secondary structure prediction

• AGADIR - An algorithm to predict the helical content of peptides
• APSSP - Advanced Protein 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)
• 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 Brunel University
• SOPMA - Geourjon and Deléage, 1995
• SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California
• 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
• MolTalk - A computational environment for structural bioinformatics
• qCOPS - navigation through fold space and the instantaneous visualization of pairwise structure similarities
• 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

Comparative modeling

• SWISS-MODEL - An automated knowledge-based protein modelling server
• 3Djigsaw - Three-dimensional models for proteins based on homologues of known structure
• CPHmodels - Automated neural-network based protein modelling server
• ESyPred3D - Automated homology modeling program using neural networks
• Geno3d - Automatic modelling of protein three-dimensional structure
• SDSC1 - Protein Structure Homology Modeling Server

Threading

• 3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit)
• Fugue - Sequence-structure homology recognition
• HHpred - Protein homology detection and structure prediction by HMM-HMM comparison
• Libellula - Neural network approach to evaluate fold recognition results
• LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
• SAM-T02 - HMM-based Protein Structure Prediction
• Threader - Protein fold recognition
• ProSup - Protein structure superimposition
• SWEET - Constructing 3D models of saccharides from their sequences

Ab initio

• HMMSTR/Rosetta - Prediction of protein structure from sequence

Assessing tertiary structure prediction

• Anolea - Atomic Non-Local Environment Assessment
• Biotech Validation Suite for Protein Structures
• EVA - EValuation of Automatic protein structure prediction
• 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
• 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

• Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures
• Ascalaph Packages
• Astex Viewer
• Jmol
• MolMol

Molecular modeling and visualization tools

• Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures
• Ascalaph Packages
• Astex Viewer
• Jmol
• MolMol
• MovieMaker - For rapid rendering of protein motions and interactions
• PyMol
• Rasmol
• VMD
• YASARA - Molecular graphics, modeling, simulations and eLearning

Prediction of disordered regions

• DisEMBL - Protein disorder prediction
• GlobPlot - Protein disorder/order/globularity/domain predictor
• List of Protein Disorder Predictors

Sequence alignment

Binary

• SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
• LALIGN - Finds multiple matching subsegments in two sequences
• Dotlet - A Java applet for sequence comparisons using the dot matrix method

Multiple

• Decrease redundancy - Reduce a set of sequences into a non-redundant set
• Nomad (Neighborhood Optimization for Multiple Alignment Discovery) - Ungapped local multiple alignment, optimized for protein sequences, even when distantly related
• CLUSTALW [At EBI, PBIL, My Hits or at EMBnet-CH]
• KALIGN - an accurate and fast multiple sequence alignment algorithm [At Karolinska Institute or at EBI]
• MAFFT [At Kyushu University, EBI or at MyHits]
• Muscle [At Berkeley or at BioAssist]
• T-Coffee [At MyHits, BioAssist or at EBI]
• MSA - at Genestream (IGH)
• DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany
• Match-Box - at University of Namur, Belgium - at Washington University
• Multalin [At INRA or at PBIL]
• MUSCA - Multiple sequence alignment using pattern discovery, at IBM

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 - 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)

Gateways

• Biosyn Gizmo - bundle of databases (siRNA, protein, peptide antigen) and tools

Phylogenetic analysis

• BIONJ - Server for NJ phylogenetic analysis
• DendroUPGMA
• PHYLIP - Server for phylogenetic analysis using the PHYLIP package
• PhyML - Server for ML phylogenetic analysis
• Phylogeny.fr - Robust Phylogenetic Analysis For The Non-Specialist
• The PhylOgenetic Web Repeater (POWER) - perform phylogenetic analysis
• BlastO - Blast on orthologous groups
• Evolutionary Trace Server (TraceSuite II) - Maps evolutionary traces to structures
• Phylogenetic programs - List of phylogenetic packages and free servers (PHYLIP pages)

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 - Gene and Protein Synonym DataBase
• MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
• XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

ExPASy Proteomics tools; Last modified 22/SEP/2008 by GGR