{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T10:21:24Z","timestamp":1773310884000,"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":[[2010,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modelling protein\u2013protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs.<\/jats:p>\n               <jats:p>Results: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs). On a GTX 285 GPU, an exhaustive and densely sampled 6D docking search can be calculated in just 15 s using multiple 1D fast Fourier transforms (FFTs). This represents a 45-fold speed-up over the corresponding calculation on a single CPU, being at least two orders of magnitude times faster than a similar CPU calculation using ZDOCK 3.0.1, and estimated to be at least three orders of magnitude faster than the GPU-accelerated version of PIPER on comparable hardware. Hence, for the first time, exhaustive FFT-based protein docking calculations may now be performed in a matter of seconds on a contemporary GPU. Three-dimensional Hex FFT correlations are also accelerated by the GPU, but the speed-up factor of only 2.5 is much less than that obtained with 1D FFTs. Thus, the Hex algorithm appears to be especially well suited to exploit GPUs compared to conventional 3D FFT docking approaches.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/hex.loria.fr\/ and http:\/\/hexserver.loria.fr\/<\/jats:p>\n               <jats:p>Contact: \u00a0dave.ritchie@loria.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq444","type":"journal-article","created":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T03:27:36Z","timestamp":1280978856000},"page":"2398-2405","source":"Crossref","is-referenced-by-count":312,"title":["Ultra-fast FFT protein docking on graphics processors"],"prefix":"10.1093","volume":"26","author":[{"given":"David W.","family":"Ritchie","sequence":"first","affiliation":[{"name":"INRIA Nancy\u2014Grand Est, LORIA, 615 Rue du Jardin Botanique, 54506 Vandoeuvre-l\u00e8s-Nancy, France"}]},{"given":"Vishwesh","family":"Venkatraman","sequence":"additional","affiliation":[{"name":"INRIA Nancy\u2014Grand Est, LORIA, 615 Rue du Jardin Botanique, 54506 Vandoeuvre-l\u00e8s-Nancy, France"}]}],"member":"286","published-online":{"date-parts":[[2010,8,4]]},"reference":[{"key":"2023012508173116600_B1","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/protein\/6.3.279","article-title":"A computer vision based technique for 3D sequence-independent structural comparison of proteins","volume":"6","author":"Bachar","year":"1993","journal-title":"Protein Eng."},{"key":"2023012508173116600_B2","volume-title":"Angular Momentum in Quantum Physics.","author":"Biedenharn","year":"1981"},{"key":"2023012508173116600_B3","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1145\/1015706.1015800","article-title":"Brook for GPUs: stream computing for graphics hardware","volume":"23","author":"Buck","year":"2004","journal-title":"ACM Trans. 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