Tools search

Rosetta docking server
GRAMM
AutoDock
Bielefeld Protein Docking.
DOCK
DOT
FTDock, RPScore and MultiDock.
Hex 3.0
ICM Protein-Protein docking
KORDO
Nussinov-Wolfson Structural Bioinformatics Group.
ZDOCK rigid-body protein-protein docking software, using a Fast Fourier Transform search algorithm.
RDOCK a refinement method to minimize energy and re-rank ZDOCK predictions.
Docking Benchmark a large set of test cases for evaluating the performance of docking algorithms.
ZDOCK Conv3D ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage.
ZDOCK Server an automated server for running ZDOCK, with capabilities for blocking and filtering contact residues.

1. 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.
2. 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
   
3. Mascot - Peptide mass fingerprint from Matrix Science Ltd., London
4. PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK
5. ProFound - Search known protein sequences with peptide mass information from Rockefeller and NY Universities [or from Genomic Solutions]
6. ProteinProspector - UCSF tools for peptide masses data (MS-Fit, MS-Pattern, MS-Digest, etc.)

1. QuickMod - Open modification spectral library search tool for identification of MS/MS data
2. Phenyx - Protein and peptide identification/characterization from MS/MS data from GeneBio, Switzerland
   
3. Mascot - Sequence query and MS/MS ion search from Matrix Science Ltd., London
4. OMSSA - MS/MS peptide spectra identification by searching libraries of known protein sequences
5. PepFrag - Search known protein sequences with peptide fragment mass information from Rockefeller and NY Universities
6. ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)

1. AACompIdent - Identify a protein by its amino acid composition
2. AACompSim - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries
3. 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
4. MultiIdent - Identify proteins with isoelectric point (pI), molecular weight (Mw), amino acid composition, sequence tag and peptide mass fingerprinting data

1. ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
2. Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
   
3. PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
4. PeptideMass - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence
   
5. xComb - computes all possible crosslinks based on proteins of interest for further interrogation using standard search engine
6. xQuest - Search machine to identify cross-linked peptides from complex samples and large protein sequence databases
7. SmileMS - Small molecule identification
8. SmileMS molecule toolkit - isotopes pattern calculator, mass to formula, mass to pubchem compounds

1. GlycanMass - Calculate the mass of an oligosaccharide structure
2. 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)
3. 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)
4. 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)

1. 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
2. MALDIPepQuant - Quantify MALDI peptides (SILAC) from Phenyx output
3. MSight - Mass Spectrometry Imager
4. pIcarver - Visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies

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

1. Translate - Translates a nucleotide sequence to a protein sequence
2. Transeq - Nucleotide to protein translation from the EMBOSS package
3. Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner
4. BCM search launcher - Six frame translation of nucleotide sequence(s)
   
5. Reverse Translate - Translates a protein sequence back to a nucleotide sequence
6. (Reverse)-Transcription and Translation Tool
   
7. Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
   

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

1. InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
2. MyHits - Relationships between protein sequences and motifs
   
3. ScanProsite - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
4. HamapScan - Scans a sequence against the HAMAP families
5. MotifScan - Scans a sequence against protein profile databases (including PROSITE)
6. Pfam HMM search - Scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre]
7. ProDom - Compares sequences with ProDom search utility
8. SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
9. FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
10. 3of5 - Complex Pattern Search - e.g. to search for a motif with 3 basic AA in 5 positions
11. ELM - Eukaryotic Linear Motif resource for functional sites in proteins
12. PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ]
13. PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
14. PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL
15. PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL
16. SMART - Simple Modular Architecture Research Tool; at EMBL
17. TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM
    
18. 9aaTAD - Prediction of Nine Amino Acid Transactivation Domain

1. ChloroP - Prediction of chloroplast transit peptides
2. LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria
3. MITOPROT - Prediction of mitochondrial targeting sequences
4. PATS - Prediction of apicoplast targeted sequences
5. PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum
6. Predotar - Prediction of mitochondrial and plastid targeting sequences
7. PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins
8. SignalP - Prediction of signal peptide cleavage sites
   
9. DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
10. NetCGlyc - C-mannosylation sites in mammalian proteins
11. NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins
12. NetGlycate - Glycation of epsilon amino groups of lysines in mammalian proteins
13. NetNGlyc - Prediction of N-glycosylation sites in human proteins
14. OGPET - Prediction of O-GalNAc (mucin-type) glycosylation sites in eukaryotic (non-protozoan) proteins
15. YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences
    
16. big-PI Predictor - GPI Modification Site Prediction
17. GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
18. Myristoylator - Prediction of N-terminal myristoylation by neural networks
19. NMT - Prediction of N-terminal N-myristoylation
20. CSS-Palm - Palmitoylation site prediction with CSS
21. PrePS - Prenylation Prediction Suite
    
22. NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
23. NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
24. NetPhosK - Kinase specific phosphorylation sites in eukaryotic proteins
25. NetPhosYeast - Serine and threonine phosphorylation sites in yeast proteins
26. GPS - Prediction of kinase-specific phosphorylation sites for 408 human protein kinases in hierarchy
27. Sulfinator - Prediction of tyrosine sulfation sites
28. SulfoSite - Prediction of tyrosine sulfation sites
29. SUMOplot - Prediction of SUMO protein attachment sites
30. SUMOsp - Prediction of sumoylation sites
31. TermiNator - Prediction of N-terminal modification (version 3)
    
32. NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
33. NetCorona - Coronavirus 3C-like proteinase cleavage sites in proteins
34. ProP - Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences

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

1. ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
2. Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
3. ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states
4. MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve
5. Scratch Protein Predictor
6. HeliQuest - A web server to screen sequences with specific alpha-helical properties
   
7. Radar - De novo repeat detection in protein sequences
8. REP - Searches a protein sequence for repeats
9. REPRO - De novo repeat detection in protein sequences
10. T-REKS - De novo detection and alignment of repeats in protein sequences
11. TRUST - De novo repeat detection in protein sequences
12. XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences
    
13. SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]
    
14. Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]
15. Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
16. Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilities with the Paircoil algorithm.
17. Multicoil - Prediction of two- and three-stranded coiled coils
18. 2ZIP - Prediction of Leucine Zippers
    
19. ePESTfind - Identification of PEST regions
    
20. HLA_Bind - Prediction of MHC type I (HLA) peptide binding
21. PEPVAC - Prediction of supertypic MHC binders
22. RANKPEP - Prediction of peptide MHC binding
23. SYFPEITHI - Prediction of MHC type I and II peptide binding
    
24. ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
25. Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
26. Peptide Builder
27. Protein Colourer - Tool for coloring your amino acid sequence
28. Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa
29. Three-/one-letter amino acid converter - Tool which converts amino acid codes from three-letter to one-letter and vice versa.
30. Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
    
31. PepDraw - peptide primary structure drawing
32. RandSeq - Random protein sequence generator

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

1. iMolTalk - An Interactive Protein Structure Analysis Server (currently down)
2. MolTalk - A computational environment for structural bioinformatics
3. COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities
4. PoPMuSiC - Prediction of thermodynamic stability changes upon point mutations; design of modified proteins
5. Seq2Struct - A web resource for the identification of sequence-structure links
6. STRAP - A structural alignment program for proteins
7. TLSMD - TLS (Translation/Libration/Screw) Motion Determination
8. TopMatch-web - Protein structure comparison

1. SWISS-MODEL - An automated knowledge-based protein modelling server
2. CPHmodels - Automated neural-network based protein modelling server
3. ESyPred3D - Automated homology modeling program using neural networks
4. Geno3d - Automatic modelling of protein three-dimensional structure

Threading

1. Phyre (Successor of 3D-PSSM) - Automated 3D model building using profile-profile matching and secondary structure
2. Fugue - Sequence-structure homology recognition
3. HHpred - Protein homology detection and structure prediction by HMM-HMM comparison
4. LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
5. SAM-T08 - HMM-based Protein Structure Prediction
6. PSIpred - Various protein structure prediction methods (including threading) at Bloomsbury Centre for Bioinformatics
   

Ab initio

1. HMMSTR/Rosetta - Prediction of protein structure from sequence

1. Anolea - Atomic Non-Local Environment Assessment
2. LiveBench - Continuous Benchmarking of Structure Prediction Servers
3. NQ-Flipper - Validation and correction of asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography
4. PROCHECK - Verification of the stereochemical quality of a protein structure
5. ProSA-web - Recognition of errors in 3D structures of proteins
6. QMEAN - Server for Model Quality Estimation
7. What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics

1. MakeMultimer - Reconstruction of multimeric molecules present in crystals
   
2. EBI PISA - Protein Interfaces, Surfaces and Assemblies
3. PQS - Protein Quaternary Structure Query form at the EBI
4. ProtBud - Comparison of asymmetric units and biological units from PDB and PQS

1. Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures
2. SwissDock - Docking of small ligands into protein active sites with EADock DSS
3. SwissParam - Topology and parameters for small molecules, for use with CHARMM and GROMAC
4. Ascalaph Packages
5. Astex Viewer
6. Jmol
7. MarvinSpace - 3D molecule visualization tool
8. MolMol
9. MovieMaker - For rapid rendering of protein motions and interactions
10. PyMol
11. Rasmol
12. SRS 3D
13. VMD
14. YASARA - Molecular graphics, modeling, simulations and eLearning

1. DisEMBL - Protein disorder prediction
2. GlobPlot - Protein disorder/order/globularity/domain predictor
3. MeDor - Metaserver or Disorder
4. POODLE - Prediction Of Order and Disorder by machine LEarning
5. List of Protein Disorder Predictors

Binary

1. LALIGN - Finds multiple matching subsegments in two sequences
2. Dotlet - A Java applet for sequence comparisons using the dot matrix method

Multiple

1. Decrease redundancy - Reduce a set of sequences into a non-redundant set
2. CLUSTALW [At EBI, PBIL, My Hits or at EMBnet-CH ]
3. KALIGN - An accurate and fast multiple sequence alignment algorithm [At Karolinska Institute or at EBI]
4. MAFFT [At Kyushu University, EBI or at MyHits ]
5. Muscle [At Berkeley or at BioAssist]
6. T-Coffee [At Vital-IT , BioAssist or at EBI]
7. MSA - at Genestream (IGH)
8. DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany
9. Match-Box - at University of Namur, Belgium - at Washington University
10. Multalin [At GenoToul Bioinfo or at PBIL]
11. MUSCA - Multiple sequence alignment using pattern discovery, at IBM

1. AMAS - Analyse Multiply Aligned Sequences
2. Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).
3. CINEMA - Color Interactive Editor for multiple alignments
4. ESPript - Tool to print a multiple alignment
5. MaxAlign - Post-processing of alignments by removing sequences (taxa) with many gaps
6. PhyloGibbs - Gibbs motif sampler incorporating phylogeny and tracking statistics
7. SVA - Sequence Variability Analyser for multiple alignments
8. PVS - A protein variability server optimized for conserved epitope discovery
   
9. WebLogo - Sequence logos at Berkeley/USA
10. plogo - Sequence logos at CBS/Denmark
11. GENIO/logo - Sequence logos at Stuttgart/Germany
12. SeqLogo - Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)

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

1. AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
2. BioMinT - Mining the biomedical literature
3. GPSDB - Gene and Protein Synonym DataBase
4. Medline Ranker
5. The Miner Suite - of bioinformatic software packages and data analysis
6. XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

1. pROC - A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves)