ExPASy Home page

Site Map

Search ExPASy

Contact us

PROSITE

Swiss-Prot

SWISS-2DPAGE

The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information).

ExPASy Proteomics tools

The tools marked by local

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

[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] [Gateways] [Phylogenetic analysis] [Biological text analysis]

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.)
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 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

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

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

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 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

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
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 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] 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 ] PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI PROSCAN - 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

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]
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 ]
PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
PROSCAN - 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 - 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

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 - 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)

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)

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 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 - protein repeats analysis TRUST - protein repeat detection method 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 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 - 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

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
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 - protein repeats analysis
TRUST - protein repeat detection method
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
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 - 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

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 COPS - 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
Homology 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 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-T02 - HMM-based Protein Structure Prediction Threader - Protein fold recognition 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 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 GenoToul Bioinfo 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

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) - Performs 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)

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) - Performs 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
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

Last modified 22/JUN/2009 by GGR

ExPASy Home page

Site Map

Search ExPASy

Contact us

PROSITE

Swiss-Prot

SWISS-2DPAGE

Hosted by

Mirror sites:

The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information).