{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T07:13:33Z","timestamp":1774768413501,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Prediction of protein\u2013protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of the initial exhaustive search. In this approach we combine the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations to accelerate the search. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. The interaction-energy minima are identified by a novel, fast and exhaustive rotational docking search combined with a simple translational scanning. Results obtained on standard protein\u2013protein benchmarks demonstrate its general applicability and robustness. The accuracy is comparable to that of existing state-of-the-art initial exhaustive rigid-body docking tools, but achieving superior efficiency. Moreover, a parallel version of the method performs the docking search in just a few minutes, opening new application opportunities in the current \u2018omics\u2019 world.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/sbg.cib.csic.es\/Software\/FRODOCK\/<\/jats:p>\n               <jats:p>Contact: \u00a0Pablo@cib.csic.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp447","type":"journal-article","created":{"date-parts":[[2009,7,21]],"date-time":"2009-07-21T00:58:23Z","timestamp":1248137903000},"page":"2544-2551","source":"Crossref","is-referenced-by-count":143,"title":["FRODOCK: a new approach for fast rotational protein\u2013protein docking"],"prefix":"10.1093","volume":"25","author":[{"given":"Jos\u00e9 Ignacio","family":"Garzon","sequence":"first","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 Ram\u00f3n","family":"Lop\u00e9z-Blanco","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carles","family":"Pons","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"},{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julio","family":"Kovacs","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruben","family":"Abagyan","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Fernandez-Recio","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Chacon","sequence":"additional","affiliation":[{"name":"1 Centro de Investigaciones Biol\u00f3gicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,7,20]]},"reference":[{"key":"2023013112122741900_B1","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-017-1120-3_14","volume-title":"Protein Structure Prediction by Global Energy Optimization.","author":"Abagyan","year":"1997"},{"key":"2023013112122741900_B2","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1006\/jmbi.1994.1052","article-title":"Biased probability Monte Carlo conformational searches and 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