{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,13]],"date-time":"2025-06-13T10:44:45Z","timestamp":1749811485533},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2012,4]]},"DOI":"10.1007\/s10822-012-9573-y","type":"journal-article","created":{"date-parts":[[2012,4,26]],"date-time":"2012-04-26T08:38:21Z","timestamp":1335429501000},"page":"451-472","source":"Crossref","is-referenced-by-count":16,"title":["Development and validation of an improved algorithm for overlaying flexible molecules"],"prefix":"10.1007","volume":"26","author":[{"given":"Robin","family":"Taylor","sequence":"first","affiliation":[]},{"given":"Jason C.","family":"Cole","sequence":"additional","affiliation":[]},{"given":"David A.","family":"Cosgrove","sequence":"additional","affiliation":[]},{"given":"Eleanor J.","family":"Gardiner","sequence":"additional","affiliation":[]},{"given":"Valerie J.","family":"Gillet","sequence":"additional","affiliation":[]},{"given":"Oliver","family":"Korb","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,4,27]]},"reference":[{"key":"9573_CR1","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1021\/jm900817u","volume":"53","author":"AR Leach","year":"2010","unstructured":"Leach AR, Gillet VJ, Lewis RA, Taylor R (2010) Three-dimensional pharmacophore methods in drug discovery. J Med Chem 53:539\u2013558","journal-title":"J Med Chem"},{"key":"9573_CR2","doi-asserted-by":"crossref","first-page":"95","DOI":"10.2174\/156802610790232260","volume":"10","author":"J Verma","year":"2010","unstructured":"Verma J, Khedkar VM, Coutinho EC (2010) 3D-QSAR in drug design\u2014a review. Curr Top Med Chem 10:95\u2013115","journal-title":"Curr Top Med Chem"},{"key":"9573_CR3","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1021\/jm0002634","volume":"44","author":"P Labute","year":"2001","unstructured":"Labute P, Williams C, Feher M, Sourial E, Schmidt JM (2001) Flexible alignment of small molecules. J Med Chem 44:1483\u20131490","journal-title":"J Med Chem"},{"key":"9573_CR4","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1007\/s10822-006-9087-6","volume":"20","author":"SL Dixon","year":"2006","unstructured":"Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20:647\u2013671","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR5","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1007\/s10822-006-9082-y","volume":"20","author":"NJ Richmond","year":"2006","unstructured":"Richmond NJ, Abrams CA, Wolohan PRN, Abrahamian E, Willett P, Clark RD (2006) GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D. J. Comput Aided Mol Des 20:567\u2013587","journal-title":"J. Comput Aided Mol Des"},{"key":"9573_CR6","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1021\/ci0503107","volume":"46","author":"SJ Cho","year":"2006","unstructured":"Cho SJ, Sun Y (2006) FLAME: a program to flexibly align molecules. J Chem Inf Model 46:298\u2013306","journal-title":"J Chem Inf Model"},{"key":"9573_CR7","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1021\/ci050427v","volume":"46","author":"J Feng","year":"2006","unstructured":"Feng J, Sanil A, Young SS (2006) PharmID: pharmacophore identification using Gibbs sampling. J Chem Inf Model 46:1352\u20131359","journal-title":"J Chem Inf Model"},{"key":"9573_CR8","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1007\/s10822-006-9078-7","volume":"20","author":"G Wolber","year":"2006","unstructured":"Wolber G, Dornhofer AA, Langer T (2006) Efficient overlay of small organic molecules using 3D pharmacophores. J Comput Aided Mol Des 20:773\u2013788","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR9","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1021\/ci6003338","volume":"47","author":"NP Todorov","year":"2007","unstructured":"Todorov NP, Alberts IL, de Esch IJP, Dean PM (2007) QUASI: a novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity. J Chem Inf Model 47:1007\u20131020","journal-title":"J Chem Inf Model"},{"key":"9573_CR10","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1021\/ci7000583","volume":"47","author":"F Zhu","year":"2007","unstructured":"Zhu F, Agrafiotis DK (2007) Recursive distance partitioning algorithm for common pharmacophore identification. J Chem Inf Model 47:1619\u20131625","journal-title":"J Chem Inf Model"},{"key":"9573_CR11","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1021\/ci600387r","volume":"47","author":"J Marialke","year":"2007","unstructured":"Marialke J, K\u00f6rner R, Tietze S, Apostolakis J (2007) Graph-based molecular alignment (GMA). J Chem Inf Model 47:591\u2013601","journal-title":"J Chem Inf Model"},{"key":"9573_CR12","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1021\/ci700395f","volume":"48","author":"AV Anghelescu","year":"2008","unstructured":"Anghelescu AV, DeLisle RK, Lowrie JF, Klon AE, Xie X, Diller DJ (2008) Technique for generating three-dimensional alignments of multiple ligands from one-dimensional alignments. J Chem Inf Model 48:1041\u20131054","journal-title":"J Chem Inf Model"},{"key":"9573_CR13","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1089\/cmb.2007.0130","volume":"15","author":"D Schneidman-Duhovny","year":"2008","unstructured":"Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ (2008) Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules. J Comput Biol 15:737\u2013754","journal-title":"J Comput Biol"},{"key":"9573_CR14","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jmgm.2008.04.003","volume":"27","author":"J Taminau","year":"2008","unstructured":"Taminau J, Thijs G, De Winter H (2008) Pharao: pharmacophore alignment and optimization. J Mol Graph Model 27:161\u2013169","journal-title":"J Mol Graph Model"},{"key":"9573_CR15","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1021\/ci100194k","volume":"50","author":"G Jones","year":"2010","unstructured":"Jones G (2010) GAPE: an improved genetic algorithm for pharmacophore elucidation. J Chem Inf Model 50:2001\u20132018","journal-title":"J Chem Inf Model"},{"key":"9573_CR16","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1021\/ci1000218","volume":"50","author":"O Korb","year":"2010","unstructured":"Korb O, Monecke P, Hessler G, St\u00fctzle T, Exner TE (2010) pharmACOphore: multiple flexible ligand alignment based on ant colony optimization. J Chem Inf Model 50:1669\u20131681","journal-title":"J Chem Inf Model"},{"key":"9573_CR17","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1007\/s10822-004-5523-7","volume":"18","author":"SJ Cottrell","year":"2004","unstructured":"Cottrell SJ, Gillet VJ, Taylor R, Wilton DJ (2004) Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques. J Comput Aided Mol Des 18:665\u2013682","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR18","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1007\/s10822-006-9086-7","volume":"20","author":"SJ Cottrell","year":"2006","unstructured":"Cottrell SJ, Gillet VJ, Taylor R (2006) Incorporating partial matches within multiobjective pharmacophore identification. J Comput Aided Mol Des 20:735\u2013749","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR19","doi-asserted-by":"crossref","first-page":"2761","DOI":"10.1021\/ci9002816","volume":"49","author":"EJ Gardiner","year":"2009","unstructured":"Gardiner EJ, Cosgrove DA, Taylor R, Gillet VJ (2009) Multiobjective optimization of pharmacophore hypotheses: bias towards low-energy conformations. J Chem Inf Model 49:2761\u20132773","journal-title":"J Chem Inf Model"},{"key":"9573_CR20","volume-title":"Multi-objective optimization using evolutionary algorithms","author":"K Deb","year":"2001","unstructured":"Deb K (2001) Multi-objective optimization using evolutionary algorithms. Wiley, Chichester"},{"key":"9573_CR21","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IH, Bourne PE (2000) The Protein Databank. Nucleic Acids Res 28:235\u2013247","journal-title":"Nucleic Acids Res"},{"key":"9573_CR22","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1021\/ci100031x","volume":"50","author":"PCD Hawkins","year":"2010","unstructured":"Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 50:572\u2013584","journal-title":"J Chem Inf Model"},{"key":"9573_CR23","first-page":"1183","volume":"D54","author":"JC Cole","year":"1998","unstructured":"Cole JC, Taylor R, Verdonk ML (1998) Directional preferences of intermolecular contacts to hydrophobic groups. Acta Crystallogr D54:1183\u20131193","journal-title":"Acta Crystallogr"},{"key":"9573_CR24","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1023\/A:1007934413448","volume":"11","author":"IJ Bruno","year":"1997","unstructured":"Bruno IJ, Cole JC, Lommerse JPM, Rowland RS, Taylor R, Verdonk ML (1997) IsoStar: a library of information about nonbonded interactions. J Comput Aided Mol Des 11:525\u2013537","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR25","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.drudis.2007.09.007","volume":"13","author":"G Wolber","year":"2008","unstructured":"Wolber G, Seidel T, Bendix F, Langer T (2008) Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug Discov Today 13:23\u201329","journal-title":"Drug Discov Today"},{"key":"9573_CR26","unstructured":"SMARTS\u2014a language for describing molecular patterns. Daylight Chemical Information Systems Inc, Aliso Viejo. http:\\\\www.daylight.com"},{"key":"9573_CR27","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1021\/ci00023a009","volume":"35","author":"R Taylor","year":"1995","unstructured":"Taylor R (1995) Simulation analysis of experimental design strategies for screening random compounds as potential new drugs and agrochemicals. J Chem Inf Comput Sci 35:59\u201367","journal-title":"J Chem Inf Comput Sci"},{"key":"9573_CR28","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1021\/ci9803381","volume":"39","author":"D Butina","year":"1999","unstructured":"Butina D (1999) Unsupervised data base clustering based on Daylight\u2019s fingerprints and Tanimoto similarity: a fast and automated way to cluster small and large data sets. J Chem Inf Comput Sci 39:747\u2013750","journal-title":"J Chem Inf Comput Sci"},{"key":"9573_CR29","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1002\/jcc.540100804","volume":"10","author":"M Clark","year":"1989","unstructured":"Clark M, Cramer RD III, Van Opdenbosch N (1989) Validation of the general purpose Tripos 5.2 force field. J Comput Chem 10:982\u20131012","journal-title":"J Comput Chem"},{"key":"9573_CR30","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/S1093-3263(02)00204-8","volume":"21","author":"J Bostr\u00f6m","year":"2003","unstructured":"Bostr\u00f6m J, Greenwood JR, Gottfries J (2003) Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graphics Model 21:449\u2013462","journal-title":"J Mol Graphics Model"},{"key":"9573_CR31","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1021\/ci200097m","volume":"51","author":"DR Koes","year":"2011","unstructured":"Koes DR, Camacho CJ (2011) Pharmer: efficient and exact pharmacophore search. J Chem Inf Model 51:1307\u20131314","journal-title":"J Chem Inf Model"},{"key":"9573_CR32","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1109\/3468.650319","volume":"28","author":"CM Fonseca","year":"1998","unstructured":"Fonseca CM, Fleming PJ (1998) Multiobjective optimisation and multiple constraint handling with evolutionary algorithms. I. A unified formulation. IEEE Trans Syst Man Cybernet A Syst Hum 28:26\u201337","journal-title":"IEEE Trans Syst Man Cybernet A Syst Hum"},{"key":"9573_CR33","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/978-3-540-44511-1_22","volume-title":"Knowledge incorporation in evolutionary computation","author":"D Cvetkovi\u0107","year":"2005","unstructured":"Cvetkovi\u0107 D, Coello CAC (2005) In: Jin Y (ed) Knowledge incorporation in evolutionary computation. Springer, New York, pp 479\u2013503"},{"key":"9573_CR34","first-page":"187","volume-title":"Modern multidimensional scaling","author":"I Borg","year":"2005","unstructured":"Borg I, Groenen PJF (2005) Modern multidimensional scaling, 2nd edn. Springer, New York, pp 187\u2013194","edition":"2"},{"key":"9573_CR35","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1023\/A:1015941316283","volume":"15","author":"M Feher","year":"2001","unstructured":"Feher M, Schmidt JM (2001) Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling. J Comput Aided Mol Des 15:1065\u20131083","journal-title":"J Comput Aided Mol Des"},{"key":"9573_CR36","doi-asserted-by":"crossref","first-page":"2214","DOI":"10.1021\/ci8002254","volume":"48","author":"ML Verdonk","year":"2008","unstructured":"Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW (2008) Protein-ligand docking against non-native protein conformers. J Chem Inf Model 48:2214\u20132225","journal-title":"J Chem Inf Model"},{"key":"9573_CR37","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/S0022-2836(02)01408-0","volume":"326","author":"M Hendlich","year":"2003","unstructured":"Hendlich M, Bergner A, G\u00fcnther J, Klebe G (2003) Relibase\u2014design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 326:607\u2013620","journal-title":"J Mol Biol"},{"key":"9573_CR38","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1021\/ci00020a039","volume":"34","author":"J Sadowski","year":"1994","unstructured":"Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inf Comput Sci 34:1000\u20131008","journal-title":"J Chem Inf Comput Sci"},{"key":"9573_CR39","unstructured":"SZYBKI\u2014molecular structure optimization in situ with MMFF94. OpenEye Scientific Software Inc, Sante Fe. http:\/\/www.eyesopen.com"},{"key":"9573_CR40","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1021\/ci050357s","volume":"46","author":"T Cheeseright","year":"2006","unstructured":"Cheeseright T, Mackey M, Rose S, Vinter A (2006) Molecular field extrema as descriptors of biological activity: definition and validation. J Chem Inf Model 46:665\u2013676","journal-title":"J Chem Inf Model"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.springerlink.com\/index\/pdf\/10.1007\/s10822-012-9573-y","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,20]],"date-time":"2017-06-20T17:54:22Z","timestamp":1497981262000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-012-9573-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4]]},"references-count":40,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2012,4]]}},"alternative-id":["9573"],"URL":"https:\/\/doi.org\/10.1007\/s10822-012-9573-y","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,4]]}}}