{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:44:03Z","timestamp":1761237843978},"reference-count":69,"publisher":"American Chemical Society (ACS)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2011,11,28]]},"DOI":"10.1021\/ci2003363","type":"journal-article","created":{"date-parts":[[2011,10,12]],"date-time":"2011-10-12T11:38:13Z","timestamp":1318419493000},"page":"2882-2896","source":"Crossref","is-referenced-by-count":18,"title":["SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design"],"prefix":"10.1021","volume":"51","author":[{"given":"Angelo D.","family":"Favia","sequence":"first","affiliation":[{"name":"Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy"}]},{"given":"Giovanni","family":"Bottegoni","sequence":"additional","affiliation":[{"name":"Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy"}]},{"given":"Irene","family":"Nobeli","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, WC1E 7HX London, United Kingdom"}]},{"given":"Paola","family":"Bisignano","sequence":"additional","affiliation":[{"name":"Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy"}]},{"given":"Andrea","family":"Cavalli","sequence":"additional","affiliation":[{"name":"Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy"},{"name":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Bologna, via Belmeloro 6, 40126 Bologna, Italy"}]}],"member":"316","published-online":{"date-parts":[[2011,10,12]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1126\/science.274.5292.1531","volume":"274","author":"Shuker S. B.","year":"1996","journal-title":"Science"},{"key":"ref2\/cit2","author":"Warr W. A.","year":"2009","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"e181","DOI":"10.1016\/j.ddtec.2010.11.012","volume":"7","author":"Retra K.","year":"2010","journal-title":"Drug Discovery Today: Technol."},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1016\/j.drudis.2009.07.013","volume":"14","author":"Dalvit C.","year":"2009","journal-title":"Drug Discovery Today"},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.drudis.2009.04.007","volume":"14","author":"Chessari G.","year":"2009","journal-title":"Drug Discovery Today"},{"key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"14859","DOI":"10.1021\/ja036166s","volume":"125","author":"Turnbull W. B.","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1021\/jm0495778","volume":"48","author":"Hartshorn M. J.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1126\/science.1096361","volume":"303","author":"Jorgensen W. L.","year":"2004","journal-title":"Science"},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/nchembio.155","volume":"5","author":"Chen Y.","year":"2009","journal-title":"Nat. Chem. Biol."},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"4212","DOI":"10.1021\/jm050355z","volume":"48","author":"Dymock B. W.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"7455","DOI":"10.1073\/pnas.0813029106","volume":"106","author":"Teotico D. G.","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"1764","DOI":"10.1158\/1535-7163.MCT-05-0524","volume":"5","author":"Warner S. L.","year":"2006","journal-title":"Mol. Cancer Ther."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1021\/ci600342e","volume":"47","author":"Marcou G.","year":"2007","journal-title":"J. Chem. Inf. Model."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"e163","DOI":"10.1016\/j.ddtec.2010.11.007","volume":"7","author":"Whittaker M.","year":"2010","journal-title":"Drug Discovery Today: Technol."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1021\/ci1000407","volume":"50","author":"Sandor M.","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1007\/s10822-009-9281-4","volume":"23","author":"Kawatkar S.","year":"2009","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref17\/cit17","volume-title":"Computational Approaches in Cheminformatics and Bioinformatics","author":"Favia A. D."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1002\/cmdc.200900078","volume":"4","author":"Friedman R.","year":"2009","journal-title":"ChemMedChem"},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1021\/ci900022h","volume":"49","author":"Gleeson M. P.","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"Jones G.","year":"1997","journal-title":"J. Mol. Biol."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"e149","DOI":"10.1016\/j.ddtec.2010.11.002","volume":"7","author":"Chen Y.","year":"2010","journal-title":"Drug Discovery Today: Technol."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/nsb1203-980","volume":"10","author":"Berman H.","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1002\/0471721204.ch13","volume":"44","author":"Orengo C. A.","year":"2003","journal-title":"Methods Biochem. Anal."},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1021\/jm061277y","volume":"50","author":"Hartshorn M. J.","year":"2007","journal-title":"J. Med. Chem."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"247","DOI":"10.2165\/00129785-200404040-00004","volume":"4","author":"Berman H. M.","year":"2004","journal-title":"Am. J. Pharmacogenomics"},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1021\/jp952516o","volume":"100","author":"Allen K. N.","year":"1996","journal-title":"J. Phys. Chem."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1038\/nchembio831","volume":"2","author":"Babaoglu K.","year":"2006","journal-title":"Nat. Chem. Biol."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/s10822-008-9188-5","volume":"22","author":"Bottegoni G.","year":"2008","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/s10822-007-9166-3","volume":"22","author":"Hawkins P. C.","year":"2008","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1021\/jm030580l","volume":"47","author":"Wang R.","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","volume":"48","author":"Wang R.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"27059","DOI":"10.1074\/jbc.M302642200","volume":"278","author":"Wimmerova M.","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1002\/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8","volume":"41","author":"Vogt J.","year":"2000","journal-title":"Proteins"},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1177\/1087057105281220","volume":"10","author":"Bernacki K.","year":"2005","journal-title":"J. Biomol. Screen."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.jmb.2007.10.065","volume":"375","author":"Favia A. D.","year":"2008","journal-title":"J. Mol. Biol."},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"15882","DOI":"10.1021\/ja065860f","volume":"128","author":"Hermann J. C.","year":"2006","journal-title":"J. Am. Chem. Soc."},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/nature05981","volume":"448","author":"Hermann J. C.","year":"2007","journal-title":"Nature"},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1021\/bi0481186","volume":"44","author":"Kalyanaraman C.","year":"2005","journal-title":"Biochemistry"},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1038\/nbt999","volume":"22","author":"Macchiarulo A.","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"D1035","DOI":"10.1093\/nar\/gkq1126","volume":"39","author":"Knox C.","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkp896","volume":"38","author":"Kanehisa M.","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"6429","DOI":"10.1021\/jm0608964","volume":"49","author":"Gasteiger J.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"6789","DOI":"10.1021\/jm0608356","volume":"49","author":"Huang N.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/j.jmgm.2011.01.004","volume":"29","author":"Durrant J. D.","year":"2011","journal-title":"J. Mol. Graphics Modell."},{"key":"ref45\/cit45","first-page":"603","volume-title":"Drug-receptor thermodynamics: introduction and applications","author":"Totrov M.","year":"2001"},{"key":"ref46\/cit46","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1002\/prot.20497","volume":"60","author":"Cole J. C.","year":"2005","journal-title":"Proteins"},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"5422","DOI":"10.1021\/jm200558u","volume":"54","author":"Verdonk M. L.","year":"2011","journal-title":"J. Med. Chem."},{"key":"ref48\/cit48","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1021\/jm030331x","volume":"47","author":"Deng Z.","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref49\/cit49","first-page":"356","volume":"11","author":"Brewerton S. C.","year":"2008","journal-title":"Curr. Opin. Drug Discovery Dev."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.drudis.2006.12.006","volume":"12","author":"Morphy R.","year":"2007","journal-title":"Drug Discovery Today"},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1021\/ci000403i","volume":"41","author":"Hann M. M.","year":"2001","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/S1359-6446(04)03069-7","volume":"9","author":"Hopkins A. L.","year":"2004","journal-title":"Drug Discovery Today"},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"D402","DOI":"10.1093\/nar\/gkq985","volume":"39","author":"Velankar S.","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1107\/S0907444904013253","volume":"60","author":"Kleywegt G. J.","year":"2004","journal-title":"Acta Crystallogr., Sect. D: Biol. Crystallogr."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"6472","DOI":"10.1021\/j100194a068","volume":"96","author":"Nemethy G.","year":"1992","journal-title":"J. Phys. Chem."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1002\/(SICI)1096-987X(199604)17:5\/6<490::AID-JCC1>3.0.CO;2-P","volume":"17","author":"Halgren T. A.","year":"1996","journal-title":"J. Comput. Chem."},{"key":"ref57\/cit57","volume-title":"QikProp","year":"2010"},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1006\/jsbi.1996.0022","volume":"116","author":"Totrov M.","year":"1996","journal-title":"J. Struct. Biol."},{"key":"ref59\/cit59","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1074\/mcp.M400159-MCP200","volume":"4","author":"An J.","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"ref60\/cit60","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1002\/prot.340190206","volume":"19","author":"Abagyan R.","year":"1994","journal-title":"Proteins"},{"key":"ref61\/cit61","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1006\/jmbi.1994.1052","volume":"235","author":"Abagyan R.","year":"1994","journal-title":"J. Mol. Biol."},{"key":"ref62\/cit62","first-page":"37","volume-title":"Proceedings of the Third Annual International Conference on Computational Molecular Biology","author":"Totrov M.","year":"1999"},{"key":"ref63\/cit63","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1021\/jm8009958","volume":"52","author":"Bottegoni G.","year":"2009","journal-title":"J. Med. Chem."},{"key":"ref64\/cit64","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1007\/978-1-60761-274-2_11","volume":"575","author":"Abagyan R.","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref65\/cit65","volume-title":"ICM Manual 3.7","author":"Abagyan R.","year":"2010"},{"key":"ref66\/cit66","volume-title":"Maestro","year":"2010"},{"key":"ref67\/cit67","volume-title":"Schr\u00f6dinger Suite 2010 Protein Preparation Wizard, Epik","year":"2010"},{"key":"ref68\/cit68","first-page":"57","volume":"17","author":"Sanner M. F.","year":"1999","journal-title":"J. Mol. Graphics Modell."},{"issue":"33","key":"ref69\/cit69","first-page":"27","volume":"14","author":"Humphrey W.","year":"1996","journal-title":"J. Mol. Graphics"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci2003363","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,13]],"date-time":"2024-04-13T16:32:39Z","timestamp":1713025959000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci2003363"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,12]]},"references-count":69,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2011,11,28]]}},"alternative-id":["10.1021\/ci2003363"],"URL":"https:\/\/doi.org\/10.1021\/ci2003363","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,12]]}}}