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Protein analysis software and databanks on the WWW

 

Protein Sequence Analysis
  • Protein identification and characterization
  • Similarity searches
  • Multiple Sequence Alignments
  • Multiple Sequence Alignment Tools
  • Pattern and profile searches
  • Primary structure analysis
  • Various Sequence Representation Tools
  • Databanks
  •  

    Protein Secondary Structure

  • Secondary Structure Prediction
  • Prediction of Transmembrane Regions
  • Databanks
  •  

    Tertiary Structure Analysis
  • Structure Prediction
  • Structure classification and analysis
  • Structure visualization
  • Databanks
  •  

    Related Journals

     

    On line courses - Tutorials

     

    Other Useful Links

     

     

    Protein Sequence Analysis

    Protein identification and characterization

    • AACompIdent - Identify a protein by its amino acid composition   http://www.expasy.ch/tools/aacomp/
    • AACompSim - Compare the amino acid composition of a SWISS-PROT entry with all other entries http://www.expasy.ch/tools/aacsim/

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    Similarity searches

    • BLAST - software for rapid and sensitive similarity searches of protein and nucleotide sequence databases http://www.ncbi.nlm.nih.gov/BLAST/
    • FASTA - searches a sequence data bank http://www.embl-heidelberg.de/cgi/fasta-wrapper-free
    • Bic -  ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator http://www2.ebi.ac.uk/bic_sw/
    • FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) http://www.ch.embnet.org/software/FDF_form.html
    • Scanps - Similarity searches using Barton's algorithm  http://www2.ebi.ac.uk/scanps/

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    Multiple Sequence Alignments

    • ClustalW - multiple sequence analysis http://www2.ebi.ac.uk/clustalw
    • SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW http://www.expasy.ch/tools/sim-prot.html
    • LALIGN - Finds multiple matching subsegments in two sequences http://www.ch.embnet.org/software/LALIGN_form.html
    • ALIGN - at Genestream (IGH) http://www2.igh.cnrs.fr/bin/align-guess.cgi
    • DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany http://bibiserv.techfak.uni-bielefeld.de/dialign/
    • Match-Box - at University of Namur, Belgium http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html

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    Multiple Sequence Alignment Tools

    • AMAS - Analyse Multiply Aligned Sequences http://barton.ebi.ac.uk/servers/amas_server.html
    • CINEMA - Color Interactive Editor for Multiple Alignments http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/
    • BOXSHADE - Pretty Printing and Shading of Multiple-Alignment Files at ISREC (Switzerland) http://www.isrec.isb-sib.ch/software/BOX_form.html

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    Pattern and profile searches

    • ScanProsite - Scans a sequence against PROSITE or a pattern against    SWISS-PROT and TrEMBL http://www.expasy.ch/tools/scnpsite.html
    • ProfileScan - Scans a sequence against protein profile databases (including PROSITE) http://www.isrec.isb-sib.ch/software/PFSCAN_form.html
    • PFAM  The Pfam database of protein domains and HMMs http://pfam.wustl.edu/
    • PRATT - Interactively generates conserved patterns from a series of unaligned proteins  http://www2.ebi.ac.uk/pratt/

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    Primary structure analysis

    • SignalP - Prediction of signal peptide cleavage sites http://www.cbs.dtu.dk/services/SignalP/
    • Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH http://www.ch.embnet.org/software/COILS_form.html
    • Paircoil - Prediction of coiled coil regions in proteins (Berger's method) http://nightingale.lcs.mit.edu/cgi-bin/score
    • PSORT - Prediction of Peptide Sorting Signals at GenomeNet (Japan) http://psort.nibb.ac.jp:8800/
    • HTH - Predicts Helix-turn-helix motifs http://pbil.ibcp.fr/NPSA/npsa_hth.html
    • Tandem Repeats Finder Identification of Tandem Repeats in Biological Sequences http://c3.biomath.mssm.edu/trf.upload.form.html

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    Various Sequence Representation Tools

    • Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence http://www.lmcp.jussieu.fr/~soyer/www-hca/hca-form.html
    • HelixWheel - Tool to represent a protein fragment as an helical wheel http://bonsai.lif.icnet.uk/people/turcotte/Java/HelixWheel/
    • The Protein Colourer - Adds residue-specific color enhancement to protein sequences at EBI (UK) http://www.ebi.ac.uk/htbin/visprot.pl

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    Databanks

    • BLOCKS - Database of Highly Conserved Regions in Proteins http://www.blocks.fhcrc.org/
    • PIRALN - Database of Protein Sequence Alignments (EMBL-Heidelberg) http://www.embl-heidelberg.de/srs/srsc?-info+PIRALN
    • Prosite - Protein families and domains http://www.expasy.ch/prosite/
    • PROTFAM - Protein Sequence Homology (Super)Families Database (MIPS) http://speedy.mips.biochem.mpg.de/mips/programs/classification.html
    • SRS - a Network Browser for Databanks in Molecular Biology http://srs.ebi.ac.uk/
    • SwissProt - annotated protein sequence database http://www.expasy.ch/

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    Protein Secondary Structure Analysis

    Secondary Structure Prediction

    • AGADIR - An algorithm to predict the helical content of peptides http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html
    • BCM PSSP - Baylor College of Medicine http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html
    • GOR - Secondary Structure Prediction (J. Garnier, J.-F. Gibrat, B. Robson) http://abs.cit.nih.gov/gor/
    • Jpred - A consensus method for protein secondary structure prediction http://jura.ebi.ac.uk:8888/
    • Predict Protein (PHD) - Predicts Aspects of Protein Structure http://dodo.cpmc.columbia.edu/predictprotein/
    • QL - Predict Secondary Structure
      • QL1 - Without homologous sequences http://abs.cit.nih.gov/ql1/
      • QL2 - With homologous sequences http://abs.cit.nih.gov/ql2/

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    Prediction of Transmembrane Regions

    • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) http://www.sbc.su.se/~miklos/DAS/
    • HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) http://www.enzim.hu/hmmtop/
    • SOSUI - Prediction of transmembrane regions (Tokyo Univ. of Agriculture & Technology) http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0E.html
    • TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) http://www.mbb.ki.se/tmap/index.html
    • TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark) http://www.cbs.dtu.dk/services/TMHMM-1.0/
    • TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH) http://www.ch.embnet.org/software/TMPRED_form.html
    • TopPred 2 - Topology prediction of membrane proteins (Stockholm University) http://www.biokemi.su.se/~server/toppred2/toppredServer.cgi

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    Databanks

    • DSSP - Database of Secondary Structure in Proteins http://www.sander.ebi.ac.uk/dssp/
    • HSSP - Homology derived Secondary Structure of Proteins http://www.sander.ebi.ac.uk:80/hssp/

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    Tertiary Structure Analysis

    Structure Prediction

    • BTPRED - prediction of location and type of beta-turns in protein sequences http://www.biochem.ucl.ac.uk/bsm/btpred/index.html
    • FOLDFIT / 3D-PSSM - Fold Recognition Servers http://bonsai.lif.icnet.uk/foldfitnew/index.html
    • FoReSST - FOld REcognition from Secondary STructure prediction (Di Francesco, Garnier, Munson) http://absalpha.dcrt.nih.gov:8008/foresst.html
    • UCLA-DOE - Structure Prediction Server http://www.doe-mbi.ucla.edu/people/frsvr/frsvr.html

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    Structure classification and analysis

    • DALI  Comparison of protein structures in 3D http://www2.ebi.ac.uk/dali
    • EBI MSD  - the European Project for the management and distribution of data on macromolecular structures http://msd.ebi.ac.uk/
    • HIC-Up Hetero-compound Information http://xray.bmc.uu.se/hicup/
    • LOOP - Protein Loop Classification http://www.icnet.uk/bmm/loop/
    • Molecules R Us - Browsing, searching and retrieval to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB) http://molbio.info.nih.gov/cgi-bin/pdb
    • Protein-Protein Interaction Server - a tool to analyse protein-protein interfaces http://www.biochem.ucl.ac.uk/bsm/PP/server/
    • SAS - Sequence alignments Annotated by Structure http://www.biochem.ucl.ac.uk/bsm/sas/
    • TOPS - Protein Topology http://tops.ebi.ac.uk/tops

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    Structure visualization

    • GRASS  Graphical Representation and Analysis of Structure Server http://trantor.bioc.columbia.edu/GRASS/surfserv_enter.cgi
    • STING - Sequence To and withIN Graphics http://trantor.bioc.columbia.edu/STING/

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    Databanks

    • Atlas of Protein Side-Chain Interactions - analysis of sidechain-sidechain interaction geometries http://www.biochem.ucl.ac.uk/bsm/sidechains/index.html
    • CATH  Class, architecture, topology and homologous superfamily http://www.biochem.ucl.ac.uk/bsm/cath/
    • Enzyme Structures Database - enzyme structures in the PDB http://www.biochem.ucl.ac.uk/bsm/enzymes/index.html
    • FSSP - Fold classification based on Structure-Structure alignment of Proteins http://www2.embl-ebi.ac.uk/dali/fssp/
    • Hydrogen Bond Atlas - atlas of side-chain and main-chain hydrogen bonding http://www.biochem.ucl.ac.uk/~mcdonald/atlas/
    • IMB Jena Image Library of Biological Macromolecules http://www.imb-jena.de/IMAGE.html
    • LPFC A Library of Protein Family Cores http://WWW-SMI.Stanford.EDU/projects/helix/LPFC/
    • OLDERADO - On Line Database of Ensemble Representative And DOmains http://neon.chem.le.ac.uk/olderado/
    • Protein Data Bank (PDB) - macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR http://www.rcsb.org/pdb/
    • PDB_select - Representative PDB structures ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/pdb_select/recent.pdb_select
    • PDBSum - Summaries and structural analyses of PDB data files http://www.biochem.ucl.ac.uk/bsm/pdbsum/
    • PROCAT - a database of 3D enzyme active site templates http://www.biochem.ucl.ac.uk/bsm/PROCAT/PROCAT.html
    • PRODOM - Protein Domain Databasehttp://protein.toulouse.inra.fr/prodom/prodom.html
    • ReLiBase - Analysis of receptor/ligand Complexes http://www2.ebi.ac.uk:8081/home.html
    • SCOP - Structural Classification of  Proteins (UK), mirrored USA and around the world http://scop.mrc-lmb.cam.ac.uk/scop/

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    Related Journals

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    On line courses - Tutorials

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    Other Useful Links
    • DIP - Database of Interacting proteins http://dip.doe-mbi.ucla.edu
    • KEGG - Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg
    • NPSA - Network Protein Sequence @nalysis : Various Sequence Analysis Tools http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_server.html
    • PROMOTIF V1.0 - Analysing protein structural motifs http://www.biochem.ucl.ac.uk/~gail/promotif/promotif.html
    • TRANSFAC- The Transcription Factor Database http://transfac.gbf.de/TRANSFAC/index.html
    • TIGR - The Institute of Genomic Research http://www.tigr.org
    • WIT - What is There? http://wit.mcs.anl.gov/WIT2/

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    Edited by Vasilis Promponas
    vprobon@cc.uoa.gr