{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T14:56:57Z","timestamp":1761058617098,"version":"3.32.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Protein\u2013protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein\u2013protein docking procedure traditionally consists of two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them.<\/jats:p><jats:p>Results: To address the second step, we developed a scoring function based on a Vorono\u00ef tessellation of the protein three-dimensional structure. We showed that the Vorono\u00ef representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein\u2013protein complexes and on decoys, and used them as attributes in several statistical learning procedures: a logistic function, Support Vector Machines (SVM), and a genetic algorithm. For the later, we used ROGER, a genetic algorithm designed to optimize the area under the receiver operating characteristics curve. To further test the scores derived with ROGER, we ranked models generated by two different docking algorithms on targets of a blind prediction experiment, improving in almost all cases the rank of native-like solutions.<\/jats:p><jats:p>Availability: \u00a0http:\/\/genomics.eu.org\/spip\/-Bioinformatics-tools-<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl654","type":"journal-article","created":{"date-parts":[[2007,1,20]],"date-time":"2007-01-20T01:12:50Z","timestamp":1169255570000},"page":"555-562","source":"Crossref","is-referenced-by-count":46,"title":["A new protein\u2013protein docking scoring function based on interface residue properties"],"prefix":"10.1093","volume":"23","author":[{"given":"J.","family":"Bernauer","sequence":"first","affiliation":[{"name":"1 Yeast Structural Genomics, IBBMC UMR CNRS 8619, B\u00e2timent 430 and 2Equipe de Bioinformatique, LRI UMR CNRS 8623, B\u00e2timent 490, Universit\u00e9 Paris-Sud, 91405 ORSAY, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Az\u00e9","sequence":"additional","affiliation":[{"name":"1 Yeast Structural Genomics, IBBMC UMR CNRS 8619, B\u00e2timent 430 and 2Equipe de Bioinformatique, LRI UMR CNRS 8623, B\u00e2timent 490, Universit\u00e9 Paris-Sud, 91405 ORSAY, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Janin","sequence":"additional","affiliation":[{"name":"1 Yeast Structural Genomics, IBBMC UMR CNRS 8619, B\u00e2timent 430 and 2Equipe de Bioinformatique, LRI UMR CNRS 8623, B\u00e2timent 490, Universit\u00e9 Paris-Sud, 91405 ORSAY, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.","family":"Poupon","sequence":"additional","affiliation":[{"name":"1 Yeast Structural Genomics, IBBMC UMR CNRS 8619, B\u00e2timent 430 and 2Equipe de Bioinformatique, LRI UMR CNRS 8623, B\u00e2timent 490, Universit\u00e9 Paris-Sud, 91405 ORSAY, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,1,18]]},"reference":[{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1088\/1478-3975\/2\/2\/S02","article-title":"A docking analysis of the statistical physics of protein-protein recognition","volume":"2","author":"Bernauer","year":"2005","journal-title":"Phys. Biol."},{"key":"2023041109374906300_","first-page":"225","article-title":"Triangulations in CGAL","author":"Boissonat","year":"2002","journal-title":"Comput. Geom. Theory Appl."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/prot.20571","article-title":"Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI","volume":"60","author":"Carter","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1002\/prot.340110406","article-title":"Protein-protein recognition analyzed by docking simulation","volume":"11","author":"Cherfils","year":"1991","journal-title":"Proteins"},{"key":"2023041109374906300_","first-page":"143","article-title":"SVMTorch: Support Vector Machines for large-scale regression problems","volume":"1","author":"Collobert","year":"2001","journal-title":"J. Mach. Learn. Res."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/prot.20555","article-title":"CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock","volume":"60","author":"Daily","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","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":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1002\/prot.20575","article-title":"Improving CAPRI predictions: optimized desolvation for rigid-body docking","volume":"60","author":"Fernandez-Recio","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"14780","DOI":"10.1074\/jbc.M414642200","article-title":"Activation of the LicT transcriptional antiterminator involves a domain swing\/lock mechanism provoking massive structural changes","volume":"280","author":"Graille","year":"2005","journal-title":"J. Biol. Chem."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"2308","DOI":"10.1093\/bioinformatics\/btg299","article-title":"PDB file parser and structure class implemented in Python","volume":"19","author":"Hamelryck","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/10618600.1996.10474713","article-title":"R: A language for data analysis and graphics","volume":"5","author":"Ihaka","year":"1996","journal-title":"J. Comput. Graph. Stat."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1002\/prot.10381","article-title":"CAPRI: a Critical Assessment of PRedicted Interactions","volume":"52","author":"Janin","year":"2003","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1002\/bip.360240307","article-title":"Reaction pathway for the quaternary structure change in hemoglobin","volume":"24","author":"Janin","year":"1985","journal-title":"Biopolymers"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1002\/prot.20574","article-title":"Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes","volume":"60","author":"Law","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1002\/prot.20567","article-title":"Study of protein-protein interaction using conformational space annealing","volume":"60","author":"Lee","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1002\/prot.20577","article-title":"Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition","volume":"60","author":"Ma","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/prot.20551","article-title":"Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures","volume":"60","author":"Mendez","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","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"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.sbi.2004.03.010","article-title":"Voronoi and Voronoi-related tessellations in studies of protein structure and interaction","volume":"14","author":"Poupon","year":"2004","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1002\/prot.10629","article-title":"Modeling structurally variable regions in homologous proteins with rosetta","volume":"55","author":"Rohl","year":"2004","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1002\/prot.20562","article-title":"Geometry-based flexible and symmetric protein docking","volume":"60","author":"Schneidman-Duhovny","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"3532","DOI":"10.1103\/PhysRevLett.85.3532","article-title":"Voronoi tessellation reveals the condensed matter character of folded proteins","volume":"85","author":"Soyer","year":"2000","journal-title":"Phys. Rev. Lett."},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1002\/prot.20572","article-title":"Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues","volume":"60","author":"Terashi","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/prot.20570","article-title":"Scoring docking models with evolutionary information","volume":"60","author":"Tress","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1002\/prot.20563","article-title":"Data-driven docking: HADDOCK's adventures in CAPRI","volume":"60","author":"van Dijk","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1002\/prot.20559","article-title":"ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5","volume":"60","author":"Wiehe","year":"2005","journal-title":"Proteins"},{"key":"2023041109374906300_","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1002\/prot.20576","article-title":"Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function","volume":"60","author":"Zhang","year":"2005","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/5\/555\/49829754\/bioinformatics_23_5_555.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/5\/555\/49829754\/bioinformatics_23_5_555.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,13]],"date-time":"2025-01-13T03:04:50Z","timestamp":1736737490000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/5\/555\/238344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,1,18]]},"references-count":29,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2007,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl654","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2007,3]]},"published":{"date-parts":[[2007,1,18]]}}}