Bioinformatics Resource Tools

Protein identification and characterization
Identification and characterization with peptide mass fingerprinting data
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.)

Identification and characterization with MS/MS data
QuickMod - Open modification spectral library search tool for identification of MS/MS data 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.)
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 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 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 SmileMS - Small molecule identification SmileMS molecule toolkit - isotopes pattern calculator, mass to formula, mass to pubchem compounds

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)
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
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

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 MyHits - 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

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) 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 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 T-REKS - De novo detection and alignment of repeats 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 probabilities 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 PepDraw - peptide primary structure drawing 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 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 NetTurnP - Prediction of Beta-turn regions in protein sequences 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 Delage, 1995 Scratch Protein Predictor 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 (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
Tertiary structure prediction
Homology modeling SWISS-MODEL - An automated knowledge-based protein modelling server 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 HMMSTR/Rosetta - Prediction of protein structure from sequence
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
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 SwissDock - Docking of small ligands into protein active sites with EADock DSS SwissParam - Topology and parameters for small molecules, for use with CHARMM and GROMAC Ascalaph Packages Astex Viewer Jmol MarvinSpace - 3D molecule visualization tool MolMol MovieMaker - For rapid rendering of protein motions and interactions PyMol Rasmol SRS 3D VMD YASARA - Molecular graphics, modeling, simulations and eLearning
Prediction of disordered regions
DisEMBL - Protein disorder prediction GlobPlot - Protein disorder/order/globularity/domain predictor MeDor - Metaserver or Disorder POODLE - Prediction Of Order and Disorder by machine LEarning List of Protein Disorder Predictors

Sequence alignment
Binary
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 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 Vital-IT , 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)

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
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

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