Protein analysis software and databanks on the WWW

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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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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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

• Bioinformatics: http://www.oup.co.uk/bioinformatics/
• Briefings in Bioinformatics.: http://www.ingenta.com/journals/browse/hsp/bib?mode=direct
• EMBO J.: http://www.emboj.org/
• FEBS: http://www.elsevier.com:80/homepage/sah/febs/
• In Silico Biology: http://www.bioinfo.de/isb/
• Journal of Computational Biology: http://www.cs.sandia.gov/jcb/
• Journal of Molecular Biology: http://www.hbuk.co.uk/jmb/
• Protein Engineering: http://protein.oupjournals.org/
• Protein Science: http://www.proteinscience.org/

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• BioInformatics Guide http://kisac.cmb.ki.se/kisac/bioinformatics/KISACbi.html
• BioComputing Hypertext Coursebook http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html
• Bioinformatics and Computational Genomics Courses at WIS http://bioinfo.weizmann.ac.il/courses/

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• 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