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1D Predictions Residue Properties, Secondary Structure Prediction, Solvent Accessibility Prediction, Transmembrane Helix Prediction, Coiled-coil Prediction, Domains and Motifs, Other Sequence Features
2D Predictions 2D Predictions
3D Predictions Homology Modelling, Fold Recognition (threading), Model Evaluation, Protein Structure Databases, Comparison and Classification
4D Predictions Programs, Protein Interaction Databases
Visualization Programs Visualization Programs
Evaluation of Prediction Methods Evaluation of Prediction Methods
Other Services More Lists of Services, Program Repositories

1D Predictions

Prediction or determination of residue characteristics along the linear sequence of the protein.

  • Residue Properties.

    • ProtScale. This tool allows the representation of a number of residue scales (hydrophobicity, beta-sheet propensities, etc.) along the sequence of the protein. http://www.expasy.ch/cgi-bin/protscale.pl

  • Secondary Structure Prediction.
    Prediction of the secondary structure state for the residues along the sequence.

    • PHDsec. http://cubic.bioc.columbia.edu/predictprotein/

    • PROF (former DSC). http://www.aber.ac.uk/~phiwww/prof/

    • Predator. http://www.embl-heidelberg.de/predator/doc_www.html

    • PSI-pred. http://www.psipred.net/

    • Agadir. Prediction of alpha-helical content of small peptides. http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

    • Consensus methods. These servers run different secondary structure prediction methods and combine the results.

      • JPred.http://jura.ebi.ac.uk:8888/

      • [email protected].http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_seccons.html

Solvent Accessibility Prediction.
Prediction of the solvent accessibility status of the residues along the sequence. Most of the methods for secondary structure prediction include also solvent accessibility prediction.

PHDsec. http://cubic.bioc.columbia.edu/predictprotein/

Transmembrane Helix Prediction.
Prediction of residues forming part of membrane spanning segments. Some of the servers predict also the orientation of the segment (N-terminal intracellular or cytoplasmic).

PHDhtm/PHDtopology. http://cubic.bioc.columbia.edu/predictprotein/

HMMTOP. http://www.enzim.hu/hmmtop/

TMpred. http://www.ch.embnet.org/software/TMPRED_form.html

TopPred 2. http://www.sbc.su.se/~erikw/toppred2/

Coiled-coil Prediction.
Prediction of coiled-coil regions. A "coiled-coil" is a super-helix formed by two of three coiled helices.

COILS. Lupas's method. http://www.ch.embnet.org/software/COILS_form.html

Multicoil. Berger's method. It also predicts the multimerization state of the coil (dimeric or trimeric). http://nightingale.lcs.mit.edu/cgi-bin/multicoil

Domains and Motifs.
Localization of domains and motifs common to known protein families.

Prosite. Biologically significant sites, patterns and profiles. http://www.expasy.ch/prosite/

Pfam. Collection of Hidden Markov Models of sequence alignments. http://www.sanger.ac.uk/Pfam/

ProDom. Collection of profiles derived from psi-blast alignments. http://protein.toulouse.inra.fr/prodom.html

Other Sequence Features.
Localization of sequence tracks known to play biologically important roles.

NetOglyc. Prediction of O-glycosilation sites. http://www.cbs.dtu.dk/services/NetOGlyc-2.0/abstract.html

PSORT. Prediction of protein sorting signals and localization sites. http://psort.nibb.ac.jp/

SignalP. Prediction of signal peptide cleavage sites. http://www.cbs.dtu.dk/services/SignalP/

ChloroP. Prediction of chloroplast transit peptides. http://www.cbs.dtu.dk/services/ChloroP/

MITOPROT . Prediction of mitochondrial targeting sequences. http://www.mips.biochem.mpg.de/cgi-bin/proj/medgen/mitofilter

big-PI. GPI Modification Site Prediction. http://mendel.imp.univie.ac.at/gpi/

NetPhos. Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins. http://www.cbs.dtu.dk/services/NetPhos/


2D Predictions

Prediction of features concerning pairs of residues, normally contacts.

PlotCorr. Calculation and interactive manipulation of residue contacts predicted by correlated mutations. http://gredos.cnb.uam.es/pazos/plotcorr.html

PDGCON. Contact prediction based on correlated mutations or other characteristics (conservation, apolarity, ...). http://www.pdg.cnb.uam.es:8081/pdg_contact_pred.html

CORNET. Contact prediction based on correlated mutations and other sequence features combined using a neural network. http://prion.biocomp.unibo.it/cornet.html


3D Predictions

Prediction of three-dimensional structure of proteins.

Homology Modelling.
For modelling the three dimensional structure of sequences with significant homology with known structures.

SWISS-MODEL. http://www.expasy.ch/swissmod/SWISS-MODEL.html

CPHmodels. http://www.cbs.dtu.dk/services/CPHmodels/

SDC1. http://cl.sdsc.edu/hm.html

Modeller. http://guitar.rockefeller.edu/modeller/modeller.html

3D-JIGSAW. http://www.bmm.icnet.uk/servers/3djigsaw/

Fold Recognition (threading).
For predicting fold type and generating low resolution models of sequences without similarity to known structures.

3D-PSSM. http://www.bmm.icnet.uk/~3dpssm/

Threader2. http://insulin.brunel.ac.uk/threader/threader.html

TOPITS (PHDthreader). http://cubic.bioc.columbia.edu/predictprotein/

SAM-T99. http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-model-library-search.html

FUGUE. http://www-cryst.bioc.cam.ac.uk/~fugue/

bioinbgu. http://www.cs.bgu.ac.il/~bioinbgu/form.html

123+. http://www-lmmb.ncifcrf.gov/~nicka/123D+.html

Threadlize. Interactive visualization and combination of threading models. http://www.cnb.uam.es/~pazos/threadlize/

Model Evaluation.
Once a model has been generated, these tools allow to evaluate its quality.

Biotech Validation Suite. Based on the tools implemented in the WhatIf program. http://biotech.embl-heidelberg.de:8400/

ProSA II. http://www.came.sbg.ac.at/Services/prosa.html

Protein Structure Databases. Comparison and Classification of Protein Structures.
The study, comparison and classification of the already known protein structures allows to extract information about sequence/family/structure relationships that can be used latter for predictions.

PDB. The database of protein structures. http://www.rcsb.org/

PDBsum. Summaries and structural analysis of PDB files. http://www.biochem.ucl.ac.uk/bsm/pdbsum/

OCA. Integration of PDB with other sources of data. http://oca.ebi.ac.uk/

SCOP. Human expert classification of protein structures. http://scop.mrc-lmb.cam.ac.uk/scop/

FSSP(Dali). Automatic classification. http://www.ebi.ac.uk/dali/

CATH. Semi-automatic classification. http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html


4D Predictions

Prediction of higher levels of protein arrangement (protein interactions).

Programs.
Programs for predicting protein-protein interactions and complexes.

AUTODOCK. Prediction of protein complexes from 3D structures. http://www.scripps.edu/pub/olson-web/doc/autodock/

DOCK. Prediction of protein complexes from 3D structures. http://www.cmpharm.ucsf.edu/kuntz/dock.html

FTdock. Prediction of protein complexes from 3D structures. http://www.bmm.icnet.uk/docking/

GRAMM. Prediction of protein complexes from 3D structures. http://reco3.musc.edu/gramm/

FlexX. Prediction of protein-ligand complexes from 3D str. It incorporates flexibility. http://cartan.gmd.de/flexx/

Protein Interaction Databases.
Studying and classifying known complexes allows to extract information that can be used later for prediction.

PQS. Study of known quaternary structures in PDB. http://pqs.ebi.ac.uk/

SPIN-PP. Study of known protein-protein interfaces in PDB. http://trantor.bioc.columbia.edu/cgi-bin/SPIN/

DIP. Database of interacting proteins. http://dip.doe-mbi.ucla.edu/

ProNet. Protein-protein interactions in Human. http://pronet.doubletwist.com/

MIPS Protein-protein interactions in Yeast (physical, genetic and others). http://www.mips.biochem.mpg.de/proj/yeast/tables/interaction/index.html


Visualization Programs

These programs allow to view and manipulate protein structures. Some of them incorporate other features like structural or sequence alignments.

RasMol Visualization program with versions for all platforms. http://wunmr.wustl.edu/EduDev/rasdir.html

Chime Plugin for visualizing structures on the web browsers. http://www.mdlchime.com/chime/

Swiss-PdbViewer Visualization and manipulation of protein structures and models. http://www.expasy.ch/spdbv/mainpage.htm


Evaluation of Prediction Methods

Due to the great number of protein structure prediction methods available on the web, it is important to asses and compare their real prediction accuracy.

CASP meetings. Expert assessment of the structure prediction methods bases on a number of targets provided by crystallographers. http://PredictionCenter.llnl.gov/

CAFASP experiments. Like CASP but for fully automatic methods only. http://www.cs.bgu.ac.il/~dfischer/CAFASP2/

EVA. Automatic and continuous evaluation. http://cubic.bioc.columbia.edu/eva/

LiveBench. Another automatic and continuous evaluation. http://BioInfo.PL/LiveBench/


Other Services

    More List of Services.
    These pages contain other collections of programs, servers and tools for sequence analysis, structure prediction, etc.

    ExPASy tools. http://www.expasy.ch/tools/

    Amos' WWW links page. By A. Bairoch. >1000 links! http://www.expasy.ch/alinks.html

    Tools for Computational Biology. By R. Sanchez & A. Pedraza. http://guitar.rockefeller.edu/~roberto/tools/tools.html

    Program Repositories.
    Links to FTP sites and repositories with free bioinformatics software.

    European Bioinformatics Institute FTP server. ftp://ftp.ebi.ac.uk/pub/software/

    EBI guided biocatalog of software. http://www.ebi.ac.uk/biocat/







    2002 ALMA Bioinformatics, SL. All rights reserved.