InterPro in 2017-beyond protein family and domain annotations

Robert D Finn; Teresa K Attwood; Patricia C Babbitt; Alex Bateman; Peer Bork; Alan J Bridge; Hsin-Yu Chang; Zsuzsanna Dosztányi; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; Gemma L Holliday; Hongzhan Huang; Xiaosong Huang; Ivica Letunic; Rodrigo Lopez; Shennan Lu; Aron Marchler-Bauer; Huaiyu Mi; Jaina Mistry; Darren A Natale; Marco Necci; Gift Nuka; Christine A Orengo; Youngmi Park; Sebastien Pesseat; Damiano Piovesan; Simon C Potter; Neil D Rawlings; Nicole Redaschi; Lorna Richardson; Catherine Rivoire; Amaia Sangrador-Vegas; Christian Sigrist; Ian Sillitoe; Ben Smithers; Silvano Squizzato; Granger Sutton; Narmada Thanki; Paul D Thomas; Silvio C E Tosatto; Cathy H Wu; Ioannis Xenarios; Lai-Su Yeh; Siew-Yit Young; Alex L Mitchell

doi:10.1093/nar/gkw1107

InterPro in 2017-beyond protein family and domain annotations

Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.

Authors

Robert D Finn¹, Teresa K Attwood², Patricia C Babbitt³, Alex Bateman⁴, Peer Bork⁵, Alan J Bridge⁶, Hsin-Yu Chang⁴, Zsuzsanna Dosztányi⁷, Sara El-Gebali⁴, Matthew Fraser⁴, Julian Gough⁸, David Haft⁹, Gemma L Holliday³, Hongzhan Huang¹⁰, Xiaosong Huang¹¹, Ivica Letunic¹², Rodrigo Lopez⁴, Shennan Lu¹³, Aron Marchler-Bauer¹³, Huaiyu Mi¹¹, Jaina Mistry⁴, Darren A Natale¹⁴, Marco Necci¹⁵, Gift Nuka⁴, Christine A Orengo¹⁶, Youngmi Park⁴, Sebastien Pesseat⁴, Damiano Piovesan¹⁵, Simon C Potter⁴, Neil D Rawlings⁴, Nicole Redaschi⁶, Lorna Richardson⁴, Catherine Rivoire⁶, Amaia Sangrador-Vegas⁴, Christian Sigrist⁶, Ian Sillitoe¹⁶, Ben Smithers⁸, Silvano Squizzato⁴, Granger Sutton⁹, Narmada Thanki¹³, Paul D Thomas¹¹, Silvio C E Tosatto^{15

17}, Cathy H Wu¹⁰, Ioannis Xenarios⁶, Lai-Su Yeh¹⁴, Siew-Yit Young⁴, Alex L Mitchell⁴

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK rdf@ebi.ac.uk.
² School of Computer Science, University of Manchester, UK.
³ Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
⁴ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁵ European Molecular Biology Laboratory, Biocomputing, Meyerhofstasse 1, 69117 Heidelberg, Germany.
⁶ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
⁷ MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, Hungary.
⁸ Computer Science department, University of Bristol, Woodland Road, Bristol BS8 1UB, UK.
⁹ Bioinformatics Department, J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, USA.
¹⁰ Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
¹¹ Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
¹² Biobyte Solutions GmbH, Bothestr. 142, 69126 Heidelberg, Germany.
¹³ National Center for Biotechnology Information, National Library of Medicine, NIH Bldg, 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
¹⁴ Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA.
¹⁵ Department of Biomedical Sciences and CRIBI Biotech Center, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.
¹⁶ Structural and Molecular Biology, University College London, Darwin Building, London WC1E 6BT, UK.
¹⁷ CNR Institute of Neuroscience, via U. Bassi 58/b, 35131 Padua, Italy.

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / methods*
Databases, Protein*
Humans
Molecular Sequence Annotation
Phylogeny
Protein Interaction Domains and Motifs*
Software*

Abstract

Publication types

MeSH terms

Grants and funding