{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:45:20Z","timestamp":1761237920470},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200\u00d7, while achieving results of similar quality.<\/jats:p>\n               <jats:p>Availability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http:\/\/mmb.pcb.ub.es\/~cpons\/Cell-Dock.<\/jats:p>\n               <jats:p>Contact: \u00a0djimenez@ac.upc.edu or juanf@bsc.es<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts454","type":"journal-article","created":{"date-parts":[[2012,7,20]],"date-time":"2012-07-20T10:12:51Z","timestamp":1342779171000},"page":"2394-2396","source":"Crossref","is-referenced-by-count":15,"title":["Cell-Dock: high-performance protein\u2013protein docking"],"prefix":"10.1093","volume":"28","author":[{"given":"Carles","family":"Pons","sequence":"first","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"},{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Jim\u00e9nez-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"},{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia","family":"Gonz\u00e1lez-\u00c1lvarez","sequence":"additional","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harald","family":"Servat","sequence":"additional","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"},{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Cabrera-Ben\u00edtez","sequence":"additional","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xavier","family":"Aguilar","sequence":"additional","affiliation":[{"name":"1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), 2Computational Bioinformatics, National Institute of Bioinformatics (INB), 3Computer Sciences Department, Barcelona Supercomputing Center (BSC), 4Computer Architecture Department, Universitat Polit\u00e8cnica de Catalunya, Barcelona 08034, Spain and 5PDC Center for High Performance Computing, KTH Royal School of Technology, Stockholm SE-100 44, 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