ExPASy Proteomics tools
2010-04-20 11:07:20| 分类：
生信分析软件
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http://ca.expasy.org/tools/#proteome
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ExPASy Proteomics tools
The tools marked by 
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] [Phylogenetic analysis] [Biological text analysis]
| 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 |
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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
- 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
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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 |
| Other tools for 2-DE data (image analysis, data publishing, etc.) |
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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
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| 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 |
| 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 |
| 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) |
| 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 - 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 HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel RandSeq - Random protein sequence generator |
| 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) 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 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 |
| 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 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 - 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
- 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
- SWEET - Constructing 3D models of saccharides from their sequences
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 - 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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| 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
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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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| 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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- Protein and peptide identification/characterization from MS/MS da
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