title: IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  moal@ebi.ac.uk.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Iain H
authors.initials: IH
authors.lastname: Moal
authors.affiliation: Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Didier
authors.initials: D
authors.lastname: Barradas-Bautista
authors.affiliation: Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Brian
authors.initials: B
authors.lastname: Jiménez-García
authors.affiliation: Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
authors.forename: Mieczyslaw
authors.initials: M
authors.lastname: Torchala
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.|Bioinformatics Program, Boston University, Boston, MA, USA.
authors.forename: Arjan
authors.initials: A
authors.lastname: van der Velde
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Thom
authors.initials: T
authors.lastname: Vreven
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.affiliation: Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Bates
authors.affiliation: Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Juan
authors.initials: J
authors.lastname: Fernández-Recio
mesh_terms: D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D062105:Molecular Docking Simulation; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software