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Bioinformatics tools most commonly used.

ADMET lab 2.0
PSE to html5
PRODIGY-binding energy
Chemical Identifier Resolver
ChemMine Web Tools
3D Nucleic Acid db

Protein secondary structure alignment at RCBS
Rosetta docking
PLIP: protein-ligand
PIMA: protein-protein interactions
PDB2PQR Server
Peptide fold model
NetPhos 3.1

PDB Europe
GRAMM-X Docking
Saccharomyces Gdb
Prediction of Intrinsically Unstructured Proteins

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Protein Docking Tools

Rosetta docking server
Bielefeld Protein Docking.
FTDock, RPScore and MultiDock.
Hex 3.0
ICM Protein-Protein docking
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.

Databases and Web servers for structure-based analysis of biological molecules



Protein Lysine Modification Database

Identification and characterization with peptide mass fingerprinting data.
  1. FindMod SIB logo - 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 SIB logo - 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.)

Identification and characterization with MS/MS data
  1. QuickMod SIB logo - Open modification spectral library search tool for identification of MS/MS data
  2. Phenyx genebio logo - 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.)

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

Other prediction or characterization tools
  1. ProtParam SIB logo - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
  2. Compute pI/Mw SIB logo - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
  3. PeptideCutter SIB logo - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
  4. PeptideMass SIB logo - 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 genebio logo - Small molecule identification
  8. SmileMS molecule toolkit genebio logoSIB logo - isotopes pattern calculator, mass to formula, mass to pubchem compounds

  1. GlycanMass SIB logo - Calculate the mass of an oligosaccharide structure
  2. GlycoMod SIB logo - 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)

Other tools for MS data (vizualisation, quantitation, analysis, etc.)
  1. HCD/CID spectra merger SIB logo - 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 SIB logo - Quantify MALDI peptides (SILAC) from Phenyx output
  3. MSight SIB logo - Mass Spectrometry Imager
  4. pIcarver SIB logo - 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.)
  1. ImageMaster / Melanie SIB logo - Software for 2-D PAGE analysis
  2. Make2D-DB II SIB logo - A package to build a web-based proteomics database

DNA - Protein
  1. Translate SIB logo - 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

Similarity searches
  1. BLAST SIB logo Network Service on ExPASy
  2. BLAST SIB logo 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

Pattern and profile searches
  1. InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
  2. MyHits SIB logo - Relationships between protein sequences and motifs
  3. ScanProsite SIB logo - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
  4. HamapScan SIB logo - Scans a sequence against the HAMAP families
  5. MotifScan SIB logo - 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 SIB logo]
  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

Post-translational modification prediction
  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 SIB logo - 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 SIB logo - 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

Topology prediction
  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 SIB logo - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
  12. TopPred - Topology prediction of membrane proteins (France)

Primary structure analysis
  1. ProtParam SIB logo - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
  2. Compute pI/Mw SIB logo - 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 SIB logo - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]
  14. Coils SIB logo - 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 SIB logo - 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 SIB logo - Random protein sequence generator

Secondary structure prediction
  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

Tertiary structure - Tertiary structure analysis
  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

Tertiary structure prediction - Homology modeling
  1. SWISS-MODEL SIB logo - 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


  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

Assessing tertiary structure prediction
  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 SIB logo - Server for Model Quality Estimation
  7. What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics

Quaternary structure
  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

Molecular modeling and visualization tools
  1. Swiss-PdbViewer SIB logo - A program to display, analyse and superimpose protein 3D structures
  2. SwissDock SIB logo - Docking of small ligands into protein active sites with EADock DSS
  3. SwissParam SIB logo - 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

Prediction of disordered regions
  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

Sequence alignment


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


  1. Decrease redundancy SIB logo - Reduce a set of sequences into a non-redundant set
  2. CLUSTALW [At EBI, PBIL, My Hits SIB logo or at EMBnet-CH SIB logo]
  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 SIB logo]
  5. Muscle [At Berkeley or at BioAssist]
  6. T-Coffee [At Vital-IT SIB logo, 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

Alignment analysis
  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 SIB logo - 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)

Phylogenetic analysis
  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. - 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)

Biological text analysis
  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 SIB logo - 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

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

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