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IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
Moal, Iain H; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A; Fernández-Recio, Juan.
Afiliação
  • Moal IH; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Barradas-Bautista D; Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
  • Jiménez-García B; Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
  • Torchala M; Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
  • van der Velde A; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
  • Vreven T; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
  • Weng Z; Bioinformatics Program, Boston University, Boston, MA, USA.
  • Bates PA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
  • Fernández-Recio J; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Bioinformatics ; 33(12): 1806-1813, 2017 Jun 15.
Article em En | MEDLINE | ID: mdl-28200016
ABSTRACT
MOTIVATION In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.

RESULTS:

Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. AVAILABILITY AND IMPLEMENTATION IRaPPA has been implemented in the SwarmDock server ( http//bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http//life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http//zdock.umassmed.edu/ ), with code available on request. CONTACT moal@ebi.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Conformação Proteica / Software / Armazenamento e Recuperação da Informação / Mapeamento de Interação de Proteínas / Simulação de Acoplamento Molecular Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2017 Tipo de documento: Article País de afiliação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Conformação Proteica / Software / Armazenamento e Recuperação da Informação / Mapeamento de Interação de Proteínas / Simulação de Acoplamento Molecular Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2017 Tipo de documento: Article País de afiliação: Reino Unido