{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:38:21Z","timestamp":1740123501715,"version":"3.37.3"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T00:00:00Z","timestamp":1472688000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR- 11-MONU-006-01"],"award-info":[{"award-number":["ANR- 11-MONU-006-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2016,9]]},"DOI":"10.1007\/s10822-016-9976-2","type":"journal-article","created":{"date-parts":[[2016,10,7]],"date-time":"2016-10-07T09:30:51Z","timestamp":1475832651000},"page":"791-804","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation"],"prefix":"10.1007","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1903-7220","authenticated-orcid":false,"given":"Sergei","family":"Grudinin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Kadukova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Eisenbarth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Marillet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Cazals","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,10,7]]},"reference":[{"key":"9976_CR1","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1021\/ci200269q","volume":"51","author":"RD Smith","year":"2011","unstructured":"Smith RD, Dunbar JJB, Ung PM, Esposito EX, Yang CY, Wang S, Carlson HA (2011) J Chem Inf Model 51:2115","journal-title":"J Chem Inf Model"},{"issue":"8","key":"9976_CR2","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1021\/ci400025f","volume":"53","author":"KL Damm-Ganamet","year":"2013","unstructured":"Damm-Ganamet KL, Smith RD, Dunbar JB Jr, Stuckey JA, Carlson HA (2013) J Chem Inf Model 53(8):1853","journal-title":"J Chem Inf Model"},{"key":"9976_CR3","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5b00339","author":"S Grudinin","year":"2015","unstructured":"Grudinin S, Popov P, Neveu E, Cheremovskiy G (2015) J Chem Inf Model. doi: 10.1021\/acs.jcim.5b00339","journal-title":"J Chem Inf Model"},{"issue":"8","key":"9976_CR4","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1021\/jm500155b","volume":"57","author":"TD Crawford","year":"2014","unstructured":"Crawford TD, Ndubaku CO, Chen H, Boggs JW, Bravo BJ, Delatorre K, Giannetti AM, Gould SE, Harris SF, Magnuson SR, McNamara E, Murray LJ, Nonomiya J, Sambrone A, Schmidt S, Smyczek T, Stanley M, Vitorino P, Wang L, West K, Wu P, Ye W (2014) J Med Chem 57(8):3484. doi: 10.1021\/jm500155b","journal-title":"J Med Chem"},{"issue":"11","key":"9976_CR5","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1002\/jcc.23218","volume":"34","author":"N Homeyer","year":"2013","unstructured":"Homeyer N, Gohlke H (2013) J Comput Chem 34(11):965","journal-title":"J Comput Chem"},{"issue":"7","key":"9976_CR6","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1021\/ja512751q","volume":"137","author":"L Wang","year":"2015","unstructured":"Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J et al (2015) J Am Chem Soc 137(7):2695","journal-title":"J Am Chem Soc"},{"issue":"6","key":"9976_CR7","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1073\/pnas.1114017109","volume":"109","author":"L Wang","year":"2012","unstructured":"Wang L, Berne B, Friesner RA (2012) PNAS 109(6):1937","journal-title":"PNAS"},{"key":"9976_CR8","doi-asserted-by":"publisher","unstructured":"Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie G, Lee C Seok, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JPGLM, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jim\u00e9nez-Garc\u00eda B, Moal IH, JF\u00e9rnandez-Recio IH, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ (2016) Proteins. doi: 10.1002\/prot.25007","DOI":"10.1002\/prot.25007"},{"issue":"10","key":"9976_CR9","doi-asserted-by":"publisher","first-page":"2242","DOI":"10.1021\/acs.jcim.5b00372","volume":"55","author":"P Popov","year":"2015","unstructured":"Popov P, Grudinin S (2015) J Chem Inf Model 55(10):2242. doi: 10.1021\/acs.jcim.5b00372","journal-title":"J Chem Inf Model"},{"key":"9976_CR10","doi-asserted-by":"publisher","unstructured":"Marillet S, Boudinot P, Cazals F (2015) Proteins: Struct Funct Bioinform 1(84): 9 (2015). doi: 10.1002\/prot.24946 . https:\/\/hal.inria.fr\/hal-01159641","DOI":"10.1002\/prot.24946"},{"key":"9976_CR11","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1002\/pro.580","volume":"20","author":"P Kastritis","year":"2011","unstructured":"Kastritis P, Moal I, Hwang H, Weng Z, Bates P, Bonvin A, Janin J (2011) Protein Sci 20:482","journal-title":"Protein Sci"},{"key":"9976_CR12","doi-asserted-by":"crossref","unstructured":"Huang SY, Zou X (2008) Proteins: Struct Funct Bioinform 72(2):557 http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.21949\/full","DOI":"10.1002\/prot.21949"},{"issue":"9","key":"9976_CR13","doi-asserted-by":"crossref","first-page":"4217","DOI":"10.1529\/biophysj.108.135814","volume":"95","author":"GY Chuang","year":"2008","unstructured":"Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S (2008) Biophys J 95(9):4217","journal-title":"Biophys J"},{"issue":"3","key":"9976_CR14","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1016\/0022-2836(92)90228-C","volume":"227","author":"VN Maiorov","year":"1992","unstructured":"Maiorov VN, Grippen GM (1992) J Mol Biol 227(3):876","journal-title":"J Mol Biol"},{"issue":"1","key":"9976_CR15","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1002\/prot.20585","volume":"61","author":"J Qiu","year":"2005","unstructured":"Qiu J, Elber R (2005) Proteins: Struct Funct Bioinform 61(1):44","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"3","key":"9976_CR16","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1002\/prot.21149","volume":"65","author":"R Rajgaria","year":"2006","unstructured":"Rajgaria R, McAllister S, Floudas C (2006) Proteins: Struct Funct Bioinform 65(3):726","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"4","key":"9976_CR17","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1002\/prot.20859","volume":"62","author":"D Tobi","year":"2006","unstructured":"Tobi D, Bahar I (2006) Proteins: Struct Funct Bioinform 62(4):970","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"2","key":"9976_CR18","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1002\/prot.22550","volume":"78","author":"D Ravikant","year":"2010","unstructured":"Ravikant D, Elber R (2010) Proteins: Struct Funct Bioinform 78(2):400","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"78","key":"9976_CR19","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1002\/prot.22626","volume":"4","author":"MH Chae","year":"2010","unstructured":"Chae MH, Krull F, Lorenzen S, Knapp EW (2010) Proteins: Struct Funct Bioinform 4(78):1026","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"7","key":"9976_CR20","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1093\/bioinformatics\/btr055","volume":"27","author":"G Neudert","year":"2011","unstructured":"Neudert G, Klebe G (2011) Bioinformatics 27(7):1021","journal-title":"Bioinformatics"},{"issue":"5","key":"9976_CR21","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1006\/jmbi.1998.2439","volume":"285","author":"L Lo Conte","year":"1999","unstructured":"Conte L Lo, Chothia C, Janin J (1999) JMB 285(5):2177","journal-title":"JMB"},{"issue":"2","key":"9976_CR22","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1017\/S0033583508004708","volume":"41","author":"J Janin","year":"2008","unstructured":"Janin J, Bahadur RP, Chakrabarti P (2008) Q Rev Biophysics 41(2):133","journal-title":"Q Rev Biophysics"},{"issue":"9","key":"9976_CR23","doi-asserted-by":"publisher","first-page":"2082","DOI":"10.1110\/ps.062245906","volume":"15","author":"F Cazals","year":"2006","unstructured":"Cazals F, Proust F, Bahadur R, Janin J (2006) Protein Sci 15(9):2082. doi: 10.1110\/ps.062245906","journal-title":"Protein Sci"},{"key":"9976_CR24","doi-asserted-by":"publisher","unstructured":"Loriot S, Cazals F (2010) Bioinformatics 26(7):964. doi: 10.1093\/bioinformatics\/btq052 . http:\/\/hal.inria.fr\/hal-00849822","DOI":"10.1093\/bioinformatics\/btq052"},{"key":"9976_CR25","first-page":"531","volume-title":"The international tables for crystallography","author":"M Gerstein","year":"2001","unstructured":"Gerstein M, Richards F (2001) Protein geometry: volumes, areas, and distances. In: Rossmann MG, Arnold E (eds) The international tables for crystallography, vol F, Chap 22. Springer, Berlin, p 531\u2013539","edition":"F, 22"},{"key":"9976_CR26","doi-asserted-by":"publisher","unstructured":"Cazals F, Kanhere H, Loriot S (2011) ACM Trans Math Softw 38(1):1. doi: 10.1145\/2049662.2049665 . http:\/\/hal.inria.fr\/hal-00849809","DOI":"10.1145\/2049662.2049665"},{"issue":"5965","key":"9976_CR27","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1126\/science.1181263","volume":"327","author":"G Meng","year":"2010","unstructured":"Meng G, Arkus N, Brenner M, Manoharan V (2010) Science 327(5965):560","journal-title":"Science"},{"issue":"11","key":"9976_CR28","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/1074-5521(95)90097-7","volume":"2","author":"J Dunitz","year":"1995","unstructured":"Dunitz J (1995) Chem Biol 2(11):709","journal-title":"Chem Biol"},{"key":"9976_CR29","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1016\/j.jmb.2014.04.017","volume":"426","author":"P Kastritis","year":"2014","unstructured":"Kastritis P, Rodrigues J, Folkers G, Boelens R, Bonvin A (2014) JMB 426:2632","journal-title":"JMB"},{"key":"9976_CR30","first-page":"217","volume":"29","author":"D Eisenberg","year":"1989","unstructured":"Eisenberg D, Wesson M, Yamashita M (1989) Chem Scr A 29:217","journal-title":"Chem Scr A"},{"key":"9976_CR31","doi-asserted-by":"publisher","unstructured":"Bouvier B, Grunberg R, Nilg\u00e8s M, Cazals F (2009) Proteins: Struct Funct Bioinform 76(3):677. doi: 10.1002\/prot.22381 . http:\/\/hal.inria.fr\/hal-00796032","DOI":"10.1002\/prot.22381"},{"key":"9976_CR32","doi-asserted-by":"publisher","unstructured":"Wang R, Fang X, Lu Y, Yang CY, Wang S (2005) J Med Chem 48(12):4111. doi: 10.1021\/jm048957q . http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15943484","DOI":"10.1021\/jm048957q"},{"key":"9976_CR33","doi-asserted-by":"publisher","unstructured":"Wang R, Fang X, Lu Y, Wang S (2004) J Med Chem 47(12):2977. doi: 10.1021\/jm030580l . http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15163179","DOI":"10.1021\/jm030580l"},{"key":"9976_CR34","doi-asserted-by":"crossref","unstructured":"Barber D (2012) Bayesian reasoning and machine learning. Cambridge University Press, Cambridge. http:\/\/assets.cambridge.org\/97805215\/18147\/cover\/9780521518147.jpg","DOI":"10.1017\/CBO9780511804779"},{"key":"9976_CR35","first-page":"1799","volume":"11","author":"S Sonnenburg","year":"2010","unstructured":"Sonnenburg S, R\u00e4tsch G, Henschel S, Widmer C, Behr J, Zien A, Bona Fd, Binder A, Gehl C, Franc V (2010) J Mach Learn Res 11:1799","journal-title":"J Mach Learn Res"},{"issue":"8","key":"9976_CR36","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1021\/acs.jcim.5b00512","volume":"56","author":"M Kadukova","year":"2016","unstructured":"Kadukova M, Grudinin S (2016) J Chem Inf Model 56(8):1410. doi: 10.1021\/acs.jcim.5b00512","journal-title":"J Chem Inf Model"},{"issue":"2","key":"9976_CR37","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) J Comput Chem 31(2):455","journal-title":"J Comput Chem"},{"issue":"5","key":"9976_CR38","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1007\/s10822-010-9352-6","volume":"24","author":"D Seeliger","year":"2010","unstructured":"Seeliger D, de Groot BL (2010) J Comput Aided Mol Des 24(5):417. doi: 10.1007\/s10822-010-9352-6","journal-title":"J Comput Aided Mol Des"},{"key":"9976_CR39","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","volume":"3","author":"NM O\u2019Boyle","year":"2011","unstructured":"O\u2019Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) J Cheminform 3:33","journal-title":"J Cheminform"},{"issue":"1","key":"9976_CR40","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.jmgm.2010.05.005","volume":"29","author":"A Heifets","year":"2010","unstructured":"Heifets A, Lilien R (2010) J Mol Graph Model 29(1):93. doi: 10.1016\/j.jmgm.2010.05.005","journal-title":"J Mol Graph Model"},{"key":"9976_CR41","unstructured":"The PyMOL Molecular Graphics System, Version 1.7 Schr\u00f6dinger, LLC"},{"key":"9976_CR42","doi-asserted-by":"crossref","unstructured":"Gy\u00f6rfi L, Krzyzak A (2002) A distribution-free theory of nonparametric regression. Springer, Berlin","DOI":"10.1007\/b97848"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9976-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-016-9976-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9976-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,19]],"date-time":"2024-06-19T20:26:16Z","timestamp":1718828776000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-016-9976-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9]]},"references-count":42,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2016,9]]}},"alternative-id":["9976"],"URL":"https:\/\/doi.org\/10.1007\/s10822-016-9976-2","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2016,9]]}}}