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ExPASy
Proteomics Tools (Mirror)
The ExPASy (the Expert
Protein Analysis System) World Wide Web server (http://www.expasy.org), is
provided as a service to the life science community by a multidisciplinary
team at the Swiss Institute of Bioinformatics (SIB). It provides access to
a variety of databases and analytical tools dedicated to proteins and
proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE,
PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are
available for specific tasks relevant to proteomics, similarity searches,
pattern and profile searches, post-translational modification prediction,
topology prediction, primary, secondary and tertiary structure analysis
and sequence alignment. These databases and tools are tightly interlinked:
a special emphasis is placed on integration of database entries with
related resources developed at the SIB and elsewhere, and the proteomics
tools have been designed to read the annotations in SWISS-PROT in order to
enhance their predictions. ExPASy started to operate in 1993, as the first
WWW server in the field of life sciences. In addition to the main site in
Switzerland, seven mirror sites in different continents currently serve
the user community.
PDF
of ExPASy:
The proteomics server for in-depth protein knowledge and analysis.
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| 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
- 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.)
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| 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.)
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| 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
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| 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
- 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
- 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
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| Other
proteomics tools |
| Glycotools |
- GlycanMass
- Calculate the mass of an oligosaccharide structure
- 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)
- 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)
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| Other
tools for MS data (vizualisation, quantitation, analysis, etc.) |
- HCD/CID
spectra merger - 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
- 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
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| Other
tools for 2-DE data (image analysis, data publishing, etc.) |
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| Similarity
searches |
- 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
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| 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
- 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
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| 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
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| 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
- Prediction of transmembrane regions and protein orientation
(EMBnet-CH)
- TopPred
- Topology prediction of membrane proteins (France)
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| 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
- 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
- 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
- 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
- RandSeq
- Random protein sequence generator
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| 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
- 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 Deléage, 1995
- Scratch
Protein Predictor
- DLP-SVM
- Domain linker prediction using SVM at Tokyo University of
Agriculture and Technology
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| 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
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| 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
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
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| 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
- Server for Model Quality Estimation
- What
If - Protein structure analysis program for mutant
prediction, structure verification, molecular graphics
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| 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
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| Molecular
modeling and visualization tools |
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| Prediction
of disordered regions |
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| 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
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| 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
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| 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)
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| 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
- 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
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