The InterPro Database and Tools for Protein Domain Analysis

Nicola J. Mulder1, Rolf Apweiler1

1 The EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, U.K.
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 2.7
DOI:  10.1002/0471250953.bi0207s21
Online Posting Date:  March, 2008
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InterPro provides a one‐stop shop for protein‐sequence classification, freeing the user from having to visit multiple databases separately and rationalize the different results in varying formats. This unit describes how to submit a sequence to InterProScan via a Web server. It also provides instructions for installing and running InterProScan locally. In addition, details on browsing InterPro families and domains of interest using the InterPro Web and sequence retrieval system (SRS) are provided to show users how to get the most from the resource. Curr. Protoc. Bioinform. 21:2.7.1‐2.7.18. © 2008 by John Wiley & Sons, Inc.

Keywords: InterPro; SRS; protein domain

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Table of Contents

  • Introduction
  • Basic Protocol 1: Protein Sequence Classification Using InterProScan via the Internet
  • Alternate Protocol 1: Local InterProScan Installation for Bulk Sequence Searches
  • Basic Protocol 2: Browsing the InterPro Database from the Web Server
  • Alternate Protocol 2: Browsing InterPro with an SRS‐Based Text Search
  • Alternate Protocol 3: Searching InterPro in SRS
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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   Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk‐Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H., and Yeats, C. 2007. New developments in the InterPro database. Nucleic Acids Res. 35: D224‐D228.
   Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural. Syst. 8: 581‐599.
   Pieper, U., Eswar, N., Davis, F.P., Braberg, H., Madhusudhan, M.S., Rossi, A., Marti‐Renom, M., Karchin, R., Webb, B.M., Eramian, D., Shen, M.Y., Kelly, L., Melo, F., and Sali, A. 2006. MODBASE: A database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34: D291‐295.
   Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. 2005. InterProScan: Protein domains identifier. Nucleic Acids Res. 33: W116‐W120.
   Scordis, P., Flower, D.R., and Attwood, T.K. 1999. FingerPRINTScan: Intelligent searching of the PRINTS motif database. Bioinformatics 15: 799‐806.
   Selengut, J.D., Haft, D.H., Davidsen, T., Ganapathy, A., Gwinn‐Giglio, M., Nelson, W.C., Richter, A.R., and White, O. 2007. TIGRFAMs and Genome Properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 35: D260‐D264.
   The UniProt Consortium. 2007. The Universal Protein Resource (UniProt). Nucleic Acids Res. 35: D193‐D197.
   Wilson, D., Madera, M., Vogel, C., Chothia, C., and Gough, J. 2007. The SUPERFAMILY database in 2007: Families and functions. Nucleic Acids Res. 35: D308‐D313.
   Wu, C.H., Nikolskaya, A., Huang, H., Yeh, L.S., Natale, D.A., Vinayaka, C.R., Hu, Z.Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R.S., Suzek, B.E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J.L., Chung, S., Castro‐Alvear, J., Dinkov, G., and Barker, W.C. 2004. PIRSF: Family classification system at the Protein Information Resource. Nucleic Acids Res. 32: D112‐D114.
   Yeats, C., Maibaum, M., Marsden, R., Dibley, M., Lee, D., Addou, S., and Orengo, C.A. 2006. Gene3D: Modelling protein structure, function and evolution. Nucleic Acids Res. 34: D281‐284.
   Zdobnov, E.M., Lopez, R., Apweiler, R., and Etzold, T. 2002. The EBI SRS server‐new features. Bioinformatics 18: 1149‐1150.
Key References
   Biswas, M., O'Rourke, J.F., Camon, E., Fraser, G., Kanapin, A., Karavidopoulou, Y., Kersey, P., Kriventseva, E., Mittard, V., Mulder, N., Phan, I., Servant, F., and Apweiler, R. 2002. Applications of InterPro in protein annotation and genome analysis. Brief. Bioinform. 3: 225‐235.
  These papers are from a special issue of Briefings in Bioinformatics on InterPro and its member databases.
   Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith‐Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Pagni, M., Peyruc, D., Ponting, C.P., Servant, F., and Sigrist, C.J.A. 2002. InterPro–An integrated documentation resource for protein families, domains and functional sites. Brief. Bioinform. 3: 285‐295.
Internet Resources
  The CATH Web site. A database of protein Class, Architecture, Topology, and Homology.
  The InterPro Web site. Integrated documentation resource for protein families, domains, and functional sites.
  The UniProt Web site. A universal Protein‐sequence database.
  The Pfam Web site. A collection of multiple sequence alignments and hidden Markov models (UNIT ).
  The ProDom Web site. An automatic compilation of homologous domains.
  The PROSITE Web site. A database of patterns and profiles describing protein families and domains (UNIT ).
  The PRINTS Web site. A compendium of protein fingerprints.
  A Simple Modular Architecture Research Tool (SMART). A collection of protein families and domains.
  The TIGRFAMs Web site. A database of protein families based on Hidden Markov Models.
  The PIRSF Database Web site. A database of protein families based on full‐length Hidden Markov Models.
  The SUPERFAMILY Web site. A database of Hidden Markov Model domains based on SCOP superfamilies.
  The Gene3D Web site. A database of Hidden Markov Model domains based on CATH superfamilies.
  The PANTHER Web site. A database of families based on Hidden Markov Models.
  Homepage for Structural Classification of Proteins (SCOP).
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