{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T02:49:58Z","timestamp":1768531798391,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Predicting how proteins interact at the molecular level is a computationally intensive task. Many protein docking algorithms begin by using fast Fourier transform (FFT) correlation techniques to find putative rigid body docking orientations. Most such approaches use 3D Cartesian grids and are therefore limited to computing three dimensional (3D) translational correlations. However, translational FFTs can speed up the calculation in only three of the six rigid body degrees of freedom, and they cannot easily incorporate prior knowledge about a complex to focus and hence further accelerate the calculation. Furthemore, several groups have developed multi-term interaction potentials and others use multi-copy approaches to simulate protein flexibility, which both add to the computational cost of FFT-based docking algorithms. Hence there is a need to develop more powerful and more versatile FFT docking techniques.<\/jats:p>\n               <jats:p>Results: This article presents a closed-form 6D spherical polar Fourier correlation expression from which arbitrary multi-dimensional multi-property multi-resolution FFT correlations may be generated. The approach is demonstrated by calculating 1D, 3D and 5D rotational correlations of 3D shape and electrostatic expansions up to polynomial order L=30 on a 2 GB personal computer. As expected, 3D correlations are found to be considerably faster than 1D correlations but, surprisingly, 5D correlations are often slower than 3D correlations. Nonetheless, we show that 5D correlations will be advantageous when calculating multi-term knowledge-based interaction potentials. When docking the 84 complexes of the Protein Docking Benchmark, blind 3D shape plus electrostatic correlations take around 30 minutes on a contemporary personal computer and find acceptable solutions within the top 20 in 16 cases. Applying a simple angular constraint to focus the calculation around the receptor binding site produces acceptable solutions within the top 20 in 28 cases. Further constraining the search to the ligand binding site gives up to 48 solutions within the top 20, with calculation times of just a few minutes per complex. Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.csd.abdn.ac.uk\/hex\/<\/jats:p>\n               <jats:p>Contact: \u00a0d.w.ritchie@abdn.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn334","type":"journal-article","created":{"date-parts":[[2008,7,1]],"date-time":"2008-07-01T00:13:23Z","timestamp":1214871203000},"page":"1865-1873","source":"Crossref","is-referenced-by-count":162,"title":["Accelerating and focusing protein\u2013protein docking correlations using multi-dimensional rotational FFT generating functions"],"prefix":"10.1093","volume":"24","author":[{"given":"David W.","family":"Ritchie","sequence":"first","affiliation":[{"name":"1 Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK and 2Department of Biomedical Engineering, University of Boston, Boston, MA, USA"}]},{"given":"Dima","family":"Kozakov","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK and 2Department of Biomedical Engineering, University of Boston, Boston, MA, USA"}]},{"given":"Sandor","family":"Vajda","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK and 2Department of Biomedical Engineering, University of Boston, Boston, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,6,30]]},"reference":[{"key":"2023020211092676400_B1","first-page":"899","article-title":"The protein data bank","volume":"D58","author":"Berman","year":"2002","journal-title":"Acta. Cryst."},{"key":"2023020211092676400_B2","volume-title":"Angular Momentum in Quantum Physics.","author":"Biedenharn","year":"1981"},{"key":"2023020211092676400_B3","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"ZDOCK: an initial-stage protein-docking algorithm","volume":"52","author":"Chen","year":"2003","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2023020211092676400_B4","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"2023020211092676400_B5","doi-asserted-by":"crossref","DOI":"10.1515\/9781400884186","volume-title":"Angular Momentum in Quantum Physics.","author":"Edmonds","year":"1957"},{"key":"2023020211092676400_B6","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1006\/jmbi.1997.1203","article-title":"Modelling protein docking using shape complementarity, electrostatics and biochemical information","volume":"272","author":"Gabb","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023020211092676400_B7","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/bioinformatics\/btl625","article-title":"ADP_EM: fast exhaustive multi-resolution docking for high throughput coverage","volume":"23","author":"Garz\u00f3n","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020211092676400_B8","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes","volume":"415","author":"Gavin","year":"2002","journal-title":"Nature"},{"key":"2023020211092676400_B9","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1016\/j.str.2004.09.014","article-title":"Complementarity of structure ensembles in protein-protein docking","volume":"12","author":"Gr\u00fcnberg","year":"2004","journal-title":"Structure"},{"key":"2023020211092676400_B10","first-page":"180","article-title":"Systematic identification of protein complexes i","volume":"415","author":"Ho","year":"2002","journal-title":"saccharomyces cerevisiae by mass spectrometry. Nature"},{"key":"2023020211092676400_B11","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome","volume":"98","author":"Ito","year":"2001","journal-title":"Proc. Natl Acad. Sci."},{"key":"2023020211092676400_B12","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1073\/pnas.89.6.2195","article-title":"Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques","volume":"89","author":"Katchalski-Katzir","year":"1992","journal-title":"Proc. Natl Acad. Sci."},{"key":"2023020211092676400_B13","first-page":"1371","article-title":"Fast rotation matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom","volume":"D59","author":"Kovacs","year":"2003","journal-title":"Acta Cryst."},{"key":"2023020211092676400_B14","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1529\/biophysj.104.058768","article-title":"Optimal clustering for detecting near-native conformations in protein docking","volume":"89","author":"Kozakov","year":"2005","journal-title":"Biophys. J."},{"key":"2023020211092676400_B15","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/prot.21117","article-title":"PIPER:an FFT-based protein docking program with pairwise potentials","volume":"65","author":"Kozakov","year":"2006","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"2023020211092676400_B16","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1093\/protein\/14.2.105","article-title":"Protein docking using continuum electrostatics and geometric fit","volume":"14","author":"Mandell","year":"2001","journal-title":"Protein Eng."},{"key":"2023020211092676400_B17","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/prot.10393","article-title":"Assessment of blind predictions of protein-protein interactions: current status of docking methods","volume":"52","author":"M\u00e9ndez","year":"2003","journal-title":"Proteins: Struct. Funct. Genet."},{"key":"2023020211092676400_B18","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/prot.20560","article-title":"Protein-protein docking benchmark 2.0: An update","volume":"60","author":"Mintseris","year":"2005","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"2023020211092676400_B19","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1002\/prot.20569","article-title":"Docking essential dynamics eigenstructures","volume":"60","author":"Mustard","year":"2005","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"2023020211092676400_B20","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1002\/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6","article-title":"Protein docking using spherical pola Fourier correlations","volume":"39","author":"Ritchie","year":"2000","journal-title":"Proteins Struct. Func. Genet."},{"key":"2023020211092676400_B21","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1002\/prot.10379","article-title":"Evaluation of protein docking predictions usin Hex 3.1 in CAPRI rounds 1 and 2","volume":"52","author":"Ritchie","year":"2003","journal-title":"Proteins: Struct. Funct. Genet."},{"key":"2023020211092676400_B22","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1107\/S002188980502474X","article-title":"High-order analytic translation matrix elements for real-space six-dimensional pola Fourier correlations","volume":"38","author":"Ritchie","year":"2005","journal-title":"J. Appl. Cryst."},{"key":"2023020211092676400_B23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2174\/138920308783565741","article-title":"Recent progress and future directions in protein-protein docking","volume":"9","author":"Ritchie","year":"2008","journal-title":"Curr. Prot. Pep. Sci."},{"key":"2023020211092676400_B24","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/j.jmb.2005.01.058","article-title":"The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking","volume":"347","author":"Smith","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2023020211092676400_B25","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein-protein interactions in saccaromyces cerevisiae","volume":"403","author":"Uetz","year":"2000","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/17\/1865\/49051416\/bioinformatics_24_17_1865.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/17\/1865\/49051416\/bioinformatics_24_17_1865.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T13:14:47Z","timestamp":1675343687000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/17\/1865\/262193"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,30]]},"references-count":25,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2008,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn334","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,9,1]]},"published":{"date-parts":[[2008,6,30]]}}}