title: Ensemble Docking from Homology Models.
abstract: We present here a systematic exploration of the quality of protein structures derived from homology modeling when used as templates for high-throughput docking. It is found that structures derived from homology modeling are often similar in quality for docking purposes than real crystal structures, even in cases where the template used to create the structural model shows only a moderate sequence identity with the protein of interest. We designed an "ensemble docking" approach based on the use of multiple homology models. The method provides results which are usually of better quality than those expected from single experimental X-ray structures. The use of this approach allows us to increase around five times the universe of use of high-throughput docking approaches for human proteins, by covering over 75% of known human therapeutic targets.
authors.affiliation: Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain, Cell and Developmental Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Institució Catalana per la Recerca i Estudis Avançats, Passeig Lluis Companys 23, Barcelona 08010, Spain, Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, and Structural Bioinformatics Node Instituto Nacional de Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Eva Maria
authors.initials: EM
authors.lastname: Novoa
authors.affiliation: Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain, Cell and Developmental Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Institució Catalana per la Recerca i Estudis Avançats, Passeig Lluis Companys 23, Barcelona 08010, Spain, Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, and Structural Bioinformatics Node Instituto Nacional de Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Lluis
authors.initials: L
authors.lastname: Ribas de Pouplana
authors.affiliation: Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain, Cell and Developmental Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Institució Catalana per la Recerca i Estudis Avançats, Passeig Lluis Companys 23, Barcelona 08010, Spain, Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, and Structural Bioinformatics Node Instituto Nacional de Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Barril
authors.affiliation: Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain, Cell and Developmental Biology, Institute for Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Institució Catalana per la Recerca i Estudis Avançats, Passeig Lluis Companys 23, Barcelona 08010, Spain, Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, and Structural Bioinformatics Node Instituto Nacional de Bioinformática, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco