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Table 10.4. Databases of patterns and sequences of protein families
Name   Web address   Description   Reference
3D-Ali http://139.91.72.10/def2/def2.html aligned protein structures and related sequences using only secondary structures assigned by author of the structures Pascarella and Argos (1992)
3DCA http://www.rlandgraf.med.ucla.edu/3DCA.html Cluster Analysis integrating structural and sequence information to obtain predictions about functionally relevant clusters of residues see Web site
3D-PSSM http://www.sbg.bio.ic.ac.uk/3dpssm uses a library of scoring matrices based on structural similarity given in the SCOP classification scheme (p. 433) for alignment with matrices based on sequence similarity Kelley et al. (2000)
BIND (Biomolecular Interaction Network Database) http://www.blueprint.org/bind/bind.php includes information on protein–protein interactions, molecular complexes, and pathways see Web site
BLOCKS http://blocks.fhcrc.org/ ungapped blocks in families defined by the Prosite catalog Henikoff and Henikoff (1996); Henikoff et al. (1998)
cluSTr http://www.ebi.ac.uk/clustr/ clustering of all proteins in PIR, TrEMBL, and SwissProt based on pair-wise similarity Kriventseva et al. (2003)
COGS (Clusters of Orthologous Groups database and search site) http://www.ncbi.nlm.nih.gov/COG clusters of similar proteins in at least three species collected from available genomic sequences Tatusov et al. (1997)
CONSURF (Protein Surface Contact Analysis) http://consurf.tau.ac.il/ mapping of functional regions on surface of proteins using conserved amino acid patterns Glaser et al. (2003)
DiffTool http://bioweb.pasteur.fr/seqanal/difftool/ clustering of proteins based in similarity Chetouani et al. (2002)
DIP (Database of Interacting Proteins) http://dip.doe-mbi.ucla.edu database of interacting proteins Xenarios et al. (2000)
eMOTIF http://dna.Stanford.EDU/emotif/ common and rare amino acid motifs in the BLOCKS and
HSSP databases
Nevill-Manning et al. (1998)
HOMSTRAD http://www-cryst.bioc.cam.ac.uk/homstrad/ structure-based alignments organized at the level of homologous familiesa Mizuguchi et al. (1998a)
HSSP http://swift.embl-heidelberg.de/hssp/ sequences similar to proteins of known structure Dodge et al. (1998)
INTERPRO resource of protein domains and functional sitesb http://www.ebi.ac.uk/interpro combination of Pfam, PRINTS, Prosite, and current SwissProt/TrEMBL sequence see Web site
LPFC http://smi-web.stanford.edu/
projects/helix/LPFC/
a library of protein family cores based on msa of protein cores using amino acid substitution matrices based on structure (see Chapter 3) see Web page
NCBI http://www.ncbi.nlm.nih.gov search conserved domain database (rpsblast) or for domain architecture (cdart) see Web page
NetOGly 2.0 server http://www.cbs.dtu.dk/services/
NetOGlyc/
predicts glycosylation sites in mammalian proteins by NN analysis Hansen et al. (1997)
NNPSL http://predict.sanger.ac.uk/nnpsl/ predicts subcellular location of proteins by NN see Web site
Pfam http://www.sanger.ac.uk/Pfam profiles derived from alignment of protein families, each one composed of similar sequence and analyzed by HMMs Sonnhammer et al. (1998)
PIR http://www-nbrf.georgetown.edu/ family and superfamily classification based on sequence alignment Barker et al. (1996)
PRINTS http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ protein fingerprints or sets of unweighted sequence motifs from aligned sequence families Attwood et al. (1999)
PROCLASS http://www-nbrf.georgetown.edu/gfserver/proclass.html database organized by Prosite patterns and PIR superfamilies; NN system for protein classification into superfamily Wu (1996); Wu et al. (1996)
PRODOM http://protein.toulouse.inra.fr/
prodom.html
groups of sequence segments or domains from similar sequences found in SwissProt database by BLASTP algorithm; aligned by msa Corpet et al. (1998)
ProtoNet http://www.protonet.cs.huji.ac.il/ automatic hierarchical clustering of SwissProt Sasson et al. (2003)
Prosite http://www.expasy.ch/prosite groups of proteins of similar biochemical function on basis of amino acid patterns Bairoch (1991); Hofmann et al. (1999)
ProtoMap http://protomap.cornell.edu classification of SwissProt and TrEMBL proteins into clusters Yona et al. (1999)
PSORT http://psort.nibb.ac.jp predicts presence of protein localization signals in proteins see Web site
SignalP Web server http://www.cbs.dtu.dk/services/
SignalP-2.0/
predicts presence and location of signal peptide cleavage sites in proteins of different organisms by NN analysis Nielsen et al. (1997)
SMART http://smart.embl-heidelberg.de database of signaling domain sequences with accurate alignments Schultz et al. (1998)
SYSTERS http://systers.molgen.mpg.de/ classification of all sequences in the SwissProt database into clusters based on sequence similarity Krause et al. (2000)
TargetDB http://targetdb.pdb.org/ database of peptides that target proteins to cellular locations see Web site
Uniprot http://www.pir.uniprot.org/ combined protein sequence database of PIR, SwissProt, and TrEMBL see Web site
    A list of Web sites with protein sequence/structure databases is maintained at http://www.imb-jena.de/ImgLibDoc/help/db/. Many protein family databases are accessible through the European Bioinformatics Institute (http://srs.ebi.ac.uk/). List of protein–protein interaction databases is maintained at http://www.hgmp.mrc.ac.uk/GenomeWeb/prot-interaction.html
    a Sequence alignments of each family shown with residues labeled by solvent accessibility, secondary structure, H bonds to main-chain amide or carbonyl group, disulfide bond, and positive Φ angle.
    b A combination of Pfam 5.0, PRINTS 25.0, Prosite 16, and current SwissProt and TrEMBL data. Additional merges with other protein pattern databases are planned.

 

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