{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T13:54:29Z","timestamp":1774014869889,"version":"3.50.1"},"reference-count":74,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,2,11]],"date-time":"2009-02-11T00:00:00Z","timestamp":1234310400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-58","type":"journal-article","created":{"date-parts":[[2009,2,11]],"date-time":"2009-02-11T19:13:42Z","timestamp":1234379622000},"source":"Crossref","is-referenced-by-count":40,"title":["An effective docking strategy for virtual screening based on multi-objective optimization algorithm"],"prefix":"10.1186","volume":"10","author":[{"given":"Honglin","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hailei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingyue","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Kang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofeng","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xicheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hualiang","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,2,11]]},"reference":[{"issue":"5665","key":"2788_CR1","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.1126\/science.1096361","volume":"303","author":"WL Jorgensen","year":"2004","unstructured":"Jorgensen WL: The many roles of computation in drug discovery. Science 2004, 303(5665):1813\u20131818. 10.1126\/science.1096361","journal-title":"Science"},{"issue":"7019","key":"2788_CR2","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nature03197","volume":"432","author":"BK Shoichet","year":"2004","unstructured":"Shoichet BK: Virtual screening of chemical libraries. Nature 2004, 432(7019):862\u2013865. 10.1038\/nature03197","journal-title":"Nature"},{"issue":"13","key":"2788_CR3","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1016\/S1359-6446(05)03484-7","volume":"10","author":"M Congreve","year":"2005","unstructured":"Congreve M, Murray CW, Blundell TL: Keynote review: Structural biology and drug discovery. Drug Discov Today 2005, 10(13):895\u2013907. 10.1016\/S1359-6446(05)03484-7","journal-title":"Drug Discov Today"},{"issue":"6","key":"2788_CR4","first-page":"497","volume":"24","author":"B Xiong","year":"2003","unstructured":"Xiong B, Gui CS, Xu XY, Luo C, Chen J, Luo HB, Chen LL, Li GW, Sun T, Yu CY, et al.: A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. Acta Pharmacol Sin 2003, 24(6):497\u2013504.","journal-title":"Acta Pharmacol Sin"},{"issue":"1","key":"2788_CR5","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/S1359-6446(04)02939-3","volume":"9","author":"T Lengauer","year":"2004","unstructured":"Lengauer T, Lemmen C, Rarey M, Zimmermann M: Novel technologies for virtual screening. Drug Discov Today 2004, 9(1):27\u201334. 10.1016\/S1359-6446(04)02939-3","journal-title":"Drug Discov Today"},{"issue":"2","key":"2788_CR6","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1147\/sj.402.0360","volume":"40","author":"Waszkowycz Bohdan","year":"2001","unstructured":"Bohdan Waszkowycz, Perkins TimDJ, Sykes RichardA, Li J: Large-scale virtual screening for discovering leads in the postgenomic era. IBM Systems J 2001, 40(2):360\u2013378.","journal-title":"IBM Systems J"},{"issue":"11","key":"2788_CR7","doi-asserted-by":"publisher","first-page":"2213","DOI":"10.1021\/jm010548w","volume":"45","author":"TN Doman","year":"2002","unstructured":"Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK: Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002, 45(11):2213\u20132221. 10.1021\/jm010548w","journal-title":"J Med Chem"},{"issue":"11","key":"2788_CR8","doi-asserted-by":"publisher","first-page":"7095","DOI":"10.1128\/JVI.79.11.7095-7103.2005","volume":"79","author":"L Chen","year":"2005","unstructured":"Chen L, Gui C, Luo X, Yang Q, Gunther S, Scandella E, Drosten C, Bai D, He X, Ludewig B, et al.: Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro. J Virol 2005, 79(11):7095\u20137103. 10.1128\/JVI.79.11.7095-7103.2005","journal-title":"J Virol"},{"issue":"11","key":"2788_CR9","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1016\/j.chembiol.2003.10.011","volume":"10","author":"H Liu","year":"2003","unstructured":"Liu H, Li Y, Song MK, Tan XJ, Cheng F, Zheng SX, Shen JH, Luo XM, Ji RY, Yue JM, et al.: Structure-based discovery of potassium channel blockers from natural products: Virtual screening and electrophysiological assay testing. Chem Biol 2003, 10(11):1103\u20131113. 10.1016\/j.chembiol.2003.10.011","journal-title":"Chem Biol"},{"issue":"4","key":"2788_CR10","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/j.cbpa.2004.05.001","volume":"8","author":"JC Alvarez","year":"2004","unstructured":"Alvarez JC: High-throughput docking as a source of novel drug leads. Curr Opin Chem Biol 2004, 8(4):365\u2013370. 10.1016\/j.cbpa.2004.05.001","journal-title":"Curr Opin Chem Biol"},{"issue":"2","key":"2788_CR11","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/0022-2836(82)90153-X","volume":"161","author":"ID Kuntz","year":"1982","unstructured":"Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE: A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982, 161(2):269\u2013288. 10.1016\/0022-2836(82)90153-X","journal-title":"J Mol Biol"},{"issue":"14","key":"2788_CR12","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","volume":"19","author":"GM Morris","year":"1998","unstructured":"Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ: Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J Comp Chem 1998, 19(14):1639\u20131662. \n                    Publisher Full Text\n                    \n                   10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","journal-title":"J Comp Chem"},{"issue":"3","key":"2788_CR13","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"G Jones","year":"1997","unstructured":"Jones G, Willett P, Glen RC, Leach AR, Taylor R: Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997, 267(3):727\u2013748. 10.1006\/jmbi.1996.0897","journal-title":"J Mol Biol"},{"issue":"7","key":"2788_CR14","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1021\/jm030644s","volume":"47","author":"TA Halgren","year":"2004","unstructured":"Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL: Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004, 47(7):1750\u20131759. 10.1021\/jm030644s","journal-title":"J Med Chem"},{"key":"2788_CR15","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1002\/(SICI)1097-0134(1997)1+<198::AID-PROT26>3.0.CO;2-I","volume":"1","author":"JS Dixon","year":"1997","unstructured":"Dixon JS: Evaluation of the CASP2 docking section. Proteins 1997, 1: 198\u2013204. \n                    Publisher Full Text\n                    \n                   10.1002\/(SICI)1097-0134(1997)1+<198::AID-PROT26>3.0.CO;2-I","journal-title":"Proteins"},{"issue":"3","key":"2788_CR16","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1021\/jm990408a","volume":"43","author":"E Perola","year":"2000","unstructured":"Perola E, Xu K, Kollmeyer TM, Kaufmann SH, Prendergast FG, Pang YP: Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads. J Med Chem 2000, 43(3):401\u2013408. 10.1021\/jm990408a","journal-title":"J Med Chem"},{"issue":"2","key":"2788_CR17","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1006\/jmbi.2001.4551","volume":"308","author":"H Claussen","year":"2001","unstructured":"Claussen H, Buning C, Rarey M, Lengauer T: FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001, 308(2):377\u2013395. 10.1006\/jmbi.2001.4551","journal-title":"J Mol Biol"},{"key":"2788_CR18","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1006\/jmbi.1996.0477","volume":"261","author":"MKB Rarey","year":"1996","unstructured":"Rarey MKB, Lengauer T, Klebe G: A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996, 261: 470\u2013489. 10.1006\/jmbi.1996.0477","journal-title":"J Mol Biol"},{"issue":"3","key":"2788_CR19","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1002\/(SICI)1097-0134(19981115)33:3<367::AID-PROT6>3.0.CO;2-W","volume":"33","author":"CA Baxter","year":"1998","unstructured":"Baxter CA, Murray CW, Clark DE, Westhead DR, Eldridge MD: Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins 1998, 33(3):367\u2013382. 10.1002\/(SICI)1097-0134(19981115)33:3<367::AID-PROT6>3.0.CO;2-W","journal-title":"Proteins"},{"key":"2788_CR20","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1023\/A:1007907728892","volume":"11","author":"RSB Colin McMartin","year":"1997","unstructured":"Colin McMartin RSB: QXP: Powerful, rapid computer algorithms for structure-based drug design. J Comput Aided Mol Des 1997, 11: 333\u2013344. 10.1023\/A:1007907728892","journal-title":"J Comput Aided Mol Des"},{"issue":"6","key":"2788_CR21","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1016\/S1074-5521(96)90093-9","volume":"3","author":"W Welch","year":"1996","unstructured":"Welch W, Ruppert J, Jain AN: Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 1996, 3(6):449\u2013462. 10.1016\/S1074-5521(96)90093-9","journal-title":"Chem Biol"},{"issue":"2","key":"2788_CR22","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/BF00119865","volume":"8","author":"MD Miller","year":"1994","unstructured":"Miller MD, Kearsley SK, Underwood DJ, Sheridan RP: FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 1994, 8(2):153\u2013174. 10.1007\/BF00119865","journal-title":"J Comput Aided Mol Des"},{"issue":"4","key":"2788_CR23","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/S1093-3263(02)00164-X","volume":"21","author":"CMJX Venkatachalam","year":"2003","unstructured":"Venkatachalam CMJX, Oldfield T, Waldman M: LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 2003, 21(4):289\u2013307. 10.1016\/S1093-3263(02)00164-X","journal-title":"J Mol Graph Model"},{"issue":"5","key":"2788_CR24","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1023\/A:1008005918983","volume":"13","author":"M Liu","year":"1999","unstructured":"Liu M, Wang S: MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J Comput Aided Mol Des 1999, 13(5):435\u2013451. 10.1023\/A:1008005918983","journal-title":"J Comput Aided Mol Des"},{"issue":"18","key":"2788_CR25","doi-asserted-by":"publisher","first-page":"4671","DOI":"10.1016\/j.bmcl.2004.06.091","volume":"14","author":"H Li","year":"2004","unstructured":"Li H, Li C, Gui C, Luo X, Chen K, Shen J, Wang X, Jiang H: GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm. Bioorg Med Chem Lett 2004, 14(18):4671\u20134676. 10.1016\/j.bmcl.2004.06.091","journal-title":"Bioorg Med Chem Lett"},{"issue":"8","key":"2788_CR26","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1016\/S0969-2126(00)00171-4","volume":"8","author":"PA Buckley","year":"2000","unstructured":"Buckley PA, Baz Jackson J, Schneider T, White SA, Rice DW, Baker PJ: Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex. Structure Fold Des 2000, 8(8):809\u2013815. 10.1016\/S0969-2126(00)00171-4","journal-title":"Structure Fold Des"},{"issue":"20","key":"2788_CR27","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1016\/S1359-6446(02)02483-2","volume":"7","author":"PD Lyne","year":"2002","unstructured":"Lyne PD: Structure-based virtual screening: an overview. Drug Discov Today 2002, 7(20):1047\u20131055. 10.1016\/S1359-6446(02)02483-2","journal-title":"Drug Discov Today"},{"issue":"11","key":"2788_CR28","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nrd1549","volume":"3","author":"DB Kitchen","year":"2004","unstructured":"Kitchen DB, Decornez H, Furr JR, Bajorath J: Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004, 3(11):935\u2013949. 10.1038\/nrd1549","journal-title":"Nat Rev Drug Discov"},{"key":"2788_CR29","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1111\/j.1749-6632.2002.tb04741.x","volume":"976","author":"J Bossuyt","year":"2002","unstructured":"Bossuyt J, Taylor BE, James-Kracke M, Hale CC: The cardiac sodium-calcium exchanger associates with caveolin-3. Ann N Y Acad Sci 2002, 976: 197\u2013204.","journal-title":"Ann N Y Acad Sci"},{"issue":"4","key":"2788_CR30","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/S1367-5931(02)00339-3","volume":"6","author":"BK Shoichet","year":"2002","unstructured":"Shoichet BK, McGovern SL, Wei BQ, Irwin JJ: Lead discovery using molecular docking. Curr Opin Chem Biol 2002, 6(4):439\u2013446. 10.1016\/S1367-5931(02)00339-3","journal-title":"Curr Opin Chem Biol"},{"issue":"12","key":"2788_CR31","doi-asserted-by":"publisher","first-page":"3032","DOI":"10.1021\/jm030489h","volume":"47","author":"P Ferrara","year":"2004","unstructured":"Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd: Assessing scoring functions for protein-ligand interactions. J Med Chem 2004, 47(12):3032\u20133047. 10.1021\/jm030489h","journal-title":"J Med Chem"},{"issue":"15","key":"2788_CR32","doi-asserted-by":"publisher","first-page":"2644","DOI":"10.1002\/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O","volume":"41","author":"HKG Gohlke","year":"2002","unstructured":"Gohlke HKG: Approaches to the description and prediction of the binding affinity of small-molecule ligands to acromolecular receptors. Angew Chem Int Ed Engl 2002, 41(15):2644\u20132676. 10.1002\/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O","journal-title":"Angew Chem Int Ed Engl"},{"key":"2788_CR33","volume-title":"The Use of Scoring Functions in Drug Discovery Applicationg","author":"H-J Boehm","year":"2002","unstructured":"Boehm H-J, Stahl M: The Use of Scoring Functions in Drug Discovery Applicationg.New York: Wiley-VCH; 2002., 18: [\n                    http:\/\/www3.interscience.wiley.com\/cgi-bin\/summary\/103020910\/SUMMARY?CRETRY=1&SRETRY=0\n                    \n                  ]"},{"issue":"25","key":"2788_CR34","doi-asserted-by":"publisher","first-page":"4759","DOI":"10.1021\/jm001044l","volume":"43","author":"C Bissantz","year":"2000","unstructured":"Bissantz C, Folkers G, Rognan D: Protein-based virtual screening of chemical databases. 1. Evaluation of different docking\/scoring combinations. J Med Chem 2000, 43(25):4759\u20134767. 10.1021\/jm001044l","journal-title":"J Med Chem"},{"issue":"25","key":"2788_CR35","doi-asserted-by":"publisher","first-page":"5100","DOI":"10.1021\/jm990352k","volume":"42","author":"PS Charifson","year":"1999","unstructured":"Charifson PS, Corkery JJ, Murcko MA, Walters WP: Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999, 42(25):5100\u20135109. 10.1021\/jm990352k","journal-title":"J Med Chem"},{"issue":"4","key":"2788_CR36","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S1093-3263(01)00125-5","volume":"20","author":"RD Clark","year":"2002","unstructured":"Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB: Consensus scoring for ligand\/protein interactions. J Mol Graph Model 2002, 20(4):281\u2013295. 10.1016\/S1093-3263(01)00125-5","journal-title":"J Mol Graph Model"},{"issue":"5","key":"2788_CR37","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1023\/B:JCAM.0000047812.39758.ab","volume":"18","author":"L Xing","year":"2004","unstructured":"Xing L, Hodgkin E, Liu Q, Sedlock D: Evaluation and application of multiple scoring functions for a virtual screening experiment. J Comput Aided Mol Des 2004, 18(5):333\u2013344. 10.1023\/B:JCAM.0000047812.39758.ab","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"2788_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1162\/evco.1995.3.1.1","volume":"3","author":"CM Fonseca","year":"1995","unstructured":"Fonseca CM, Fleming PJ: An overview of evolutionary algorithms in multiobjecitive optimization. Evol Comput 1995, 3(1):1\u201316. 10.1162\/evco.1995.3.1.1","journal-title":"Evol Comput"},{"issue":"2","key":"2788_CR39","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1021\/ci010375j","volume":"42","author":"VJKW Gillet","year":"2002","unstructured":"Gillet VJKW, Willett P, Fleming PJ, Green DV: Combinatorial library design using a multiobjective genetic algorithm. J Chem Inf Comput Sci 2002, 42(2):375\u2013385.","journal-title":"J Chem Inf Comput Sci"},{"issue":"2","key":"2788_CR40","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1021\/ci970438r","volume":"38","author":"S Handschuh","year":"1998","unstructured":"Handschuh S, Wagener M, Gasteiger J: Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method. J Chem Inf Comput Sci 1998, 38(2):220\u2013232.","journal-title":"J Chem Inf Comput Sci"},{"key":"2788_CR41","volume-title":"PhD thesis","author":"E Zitzler","year":"1999","unstructured":"Zitzler E: Evolutionary Algorithms for Multiobjective Optimization: Methods and Applications. PhD thesis. Zurich, Switzerland,: Swiss Federal Institute of Technology (ETH); 1999."},{"key":"2788_CR42","volume-title":"PhD thesis","author":"CAC Coello","year":"1996","unstructured":"Coello CAC: An Empirical Study of Evolutionary Techniques for Multiobjective Optimization in Engineering Design. PhD thesis. New Orleans, Louisiana,: Tulane University; 1996."},{"issue":"2","key":"2788_CR43","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1162\/106365600568202","volume":"8","author":"E Zitzler","year":"2000","unstructured":"Zitzler E, Deb K, Thiele L: Comparison of Multiobjective Evolutionary Algorithms: Empirical Results. Evol Comput 2000, 8(2):173\u2013195. 10.1162\/106365600568202","journal-title":"Evol Comput"},{"key":"2788_CR44","first-page":"109","volume-title":"ACM Comput surveys: 2000","author":"CAC Coello","year":"2000","unstructured":"Coello CAC: An undated survey of GA-based multiobjective optimization techniques. ACM Comput surveys: 2000 2000, 109\u2013143. 10.1145\/358923.358929"},{"key":"2788_CR45","volume-title":"Multi-Objective Optimization using Evolutionary Algorithms","author":"K Deb","year":"2001","unstructured":"Deb K: Multi-Objective Optimization using Evolutionary Algorithms. Chichester, UK,: John Wiley & Sons; 2001."},{"key":"2788_CR46","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1146\/annurev.biophys.32.110601.142532","volume":"32","author":"N Brooijmans","year":"2003","unstructured":"Brooijmans N, Kuntz ID: Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 2003, 32: 335\u2013373. 10.1146\/annurev.biophys.32.110601.142532","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"Pt 6 No 1","key":"2788_CR47","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1107\/S0907444902003451","volume":"58","author":"HM Berman","year":"2002","unstructured":"Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, et al.: The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002, 58(Pt 6 No 1):899\u2013907. 10.1107\/S0907444902003451","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2788_CR48","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1016\/0022-2836(92)91054-S","volume":"226","author":"H Brandstetter","year":"1992","unstructured":"Brandstetter H, Turk D, Hoeffken HW, Grosse D, Sturzebecher J, Martin PD, Edwards BF, Bode W: Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. J Mol Biol 1992, 226: 1085. 10.1016\/0022-2836(92)91054-S","journal-title":"J Mol Biol"},{"key":"2788_CR49","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1016\/S0092-8674(00)81717-1","volume":"95","author":"AK Shiau","year":"1998","unstructured":"Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL: The structural basis of estrogen receptor\/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998, 95: 927. 10.1016\/S0092-8674(00)81717-1","journal-title":"Cell"},{"key":"2788_CR50","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/384644a0","volume":"384","author":"RG Kurumbail","year":"1996","unstructured":"Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, Pak JY, Gildehaus D, Miyashiro JM, Penning TD, Seibert K, Isakson PC, Stallings WC: Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature 1996, 384: 644. 10.1038\/384644a0","journal-title":"Nature"},{"key":"2788_CR51","doi-asserted-by":"publisher","first-page":"3219","DOI":"10.1016\/0040-4020(80)80168-2","volume":"36","author":"J Gasteiger","year":"1980","unstructured":"Gasteiger J, Marsili M: Iterative partial equalization of orbital electronegativity \u2013 a rapid access to atomic charges. Tetrahedron 1980, 36: 3219\u20133228. 10.1016\/0040-4020(80)80168-2","journal-title":"Tetrahedron"},{"key":"2788_CR52","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1002\/jcc.540130412","volume":"13","author":"EC Meng","year":"1992","unstructured":"Meng EC, Shoichet BK, Kuntz ID: Automated docking with grid-based energy evaluation. J Comp Chem 1992, 13: 504\u2013524.","journal-title":"J Comp Chem"},{"issue":"9","key":"2788_CR53","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1002\/(SICI)1096-987X(19970715)18:9<1175::AID-JCC6>3.0.CO;2-O","volume":"18","author":"TJA Ewing","year":"1997","unstructured":"Ewing TJA, Kuntz ID: Critical evaluation of search algorithms used in automated molecular docking. J Comp Chem 1997, 18(9):1175\u20131189. \n                    Publisher Full Text\n                    \n                   10.1002\/(SICI)1096-987X(19970715)18:9<1175::AID-JCC6>3.0.CO;2-O","journal-title":"J Comp Chem"},{"issue":"5","key":"2788_CR54","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1023\/A:1011115820450","volume":"15","author":"TJ Ewing","year":"2001","unstructured":"Ewing TJ, Makino S, Skillman AG, Kuntz ID: DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001, 15(5):411\u2013428. 10.1023\/A:1011115820450","journal-title":"J Comput Aided Mol Des"},{"key":"2788_CR55","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1002\/jcc.540070216","volume":"7","author":"SJ Weiner","year":"1986","unstructured":"Weiner SJ, Kollman PA, Nguyen DT, Case DA: A New force filed for molecular mechanical simulation of nucleic acids and proteins. J Comp Chem 1986, 7: 230\u2013252. 10.1002\/jcc.540070216","journal-title":"J Comp Chem"},{"issue":"2","key":"2788_CR56","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/S0022-2836(02)00777-5","volume":"322","author":"BQ Wei","year":"2002","unstructured":"Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK: A model binding site for testing scoring functions in molecular docking. J Mol Biol 2002, 322(2):339\u2013355. 10.1016\/S0022-2836(02)00777-5","journal-title":"J Mol Biol"},{"issue":"3","key":"2788_CR57","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1162\/106365602760234108","volume":"10","author":"M Laumanns","year":"2002","unstructured":"Laumanns M, Thiele L, Deb K, Zitzler E: Combining convergence and diversity in evolutionary multi-objective optimization. Evol Comput 2002, 10(3):263\u2013282. 10.1162\/106365602760234108","journal-title":"Evol Comput"},{"key":"2788_CR58","volume-title":"KanGAL Report","author":"K Deb","year":"2003","unstructured":"Deb K, Mohan M, Mishra S: A Fast Multi-objective Evolutionary Algorithm for Finding Well-Spread Pareto-Optimal Solutions. KanGAL Report 2003., No. 2003002:"},{"issue":"2","key":"2788_CR59","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1006\/jmbi.1999.3371","volume":"295","author":"H Gohlke","year":"2000","unstructured":"Gohlke H, Hendlich M, Klebe G: Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000, 295(2):337\u2013356. 10.1006\/jmbi.1999.3371","journal-title":"J Mol Biol"},{"issue":"3","key":"2788_CR60","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1002\/(SICI)1097-0134(19991115)37:3<334::AID-PROT3>3.0.CO;2-9","volume":"37","author":"RM Knegtel","year":"1999","unstructured":"Knegtel RM, Wagener M: Efficacy and selectivity in flexible database docking. Proteins 1999, 37(3):334\u2013345. 10.1002\/(SICI)1097-0134(19991115)37:3<334::AID-PROT3>3.0.CO;2-9","journal-title":"Proteins"},{"issue":"1","key":"2788_CR61","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10822-008-9232-5","volume":"23","author":"L Kang","year":"2009","unstructured":"Kang L, Li H, Jiang H, Wang X: An improved adaptive genetic algorithm for protein-ligand docking. J Comput Aided Mol Des 2009, 23(1):1\u201312. 10.1007\/s10822-008-9232-5","journal-title":"J Comput Aided Mol Des"},{"key":"2788_CR62","volume-title":"Information Theory, Inference, and Learning Algorithms","author":"DJC Mackay","year":"2003","unstructured":"Mackay DJC: Information Theory, Inference, and Learning Algorithms. Cambridge: Cambridge University Press; 2003."},{"key":"2788_CR63","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.plrev.2004.01.002","volume":"1","author":"C Adami","year":"2004","unstructured":"Adami C: Information Theory in Molecular Biology. Phys Life Rev 2004, 1: 3\u201322. 10.1016\/j.plrev.2004.01.002","journal-title":"Phys Life Rev"},{"issue":"4","key":"2788_CR64","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1002\/prot.21367","volume":"67","author":"A Grosdidier","year":"2007","unstructured":"Grosdidier A, Zoete V, Michielin O: EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins 2007, 67(4):1010\u20131025. 10.1002\/prot.21367","journal-title":"Proteins"},{"issue":"1","key":"2788_CR65","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s00894-002-0112-y","volume":"9","author":"T Schulz-Gasch","year":"2003","unstructured":"Schulz-Gasch T, Stahl M: Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J Mol Model 2003, 9(1):47\u201357.","journal-title":"J Mol Model"},{"issue":"14","key":"2788_CR66","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1021\/jm990073x","volume":"42","author":"I Muegge","year":"1999","unstructured":"Muegge I, Martin YC, Hajduk PJ, Fesik SW: Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 1999, 42(14):2498\u20132503. 10.1021\/jm990073x","journal-title":"J Med Chem"},{"issue":"5","key":"2788_CR67","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1021\/jm980536j","volume":"42","author":"I Muegge","year":"1999","unstructured":"Muegge I, Martin YC: A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 1999, 42(5):791\u2013804. 10.1021\/jm980536j","journal-title":"J Med Chem"},{"issue":"22","key":"2788_CR68","doi-asserted-by":"publisher","first-page":"3267","DOI":"10.1039\/b409570g","volume":"2","author":"PM Marsden","year":"2004","unstructured":"Marsden PM, Puvanendrampillai D, Mitchell JB, Glen RC: Predicting protein-ligand binding affinities: a low scoring game? Org Biomol Chem 2004, 2(22):3267\u20133273. 10.1039\/b409570g","journal-title":"Org Biomol Chem"},{"issue":"7","key":"2788_CR69","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1021\/jm0003992","volume":"44","author":"M Stahl","year":"2001","unstructured":"Stahl M, Rarey M: Detailed analysis of scoring functions for virtual screening. J Med Chem 2001, 44(7):1035\u20131042. 10.1021\/jm0003992","journal-title":"J Med Chem"},{"issue":"6","key":"2788_CR70","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1023\/A:1008015827877","volume":"13","author":"CW Murray","year":"1999","unstructured":"Murray CW, Baxter CA, Frenkel AD: The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des 1999, 13(6):547\u2013562. 10.1023\/A:1008015827877","journal-title":"J Comput Aided Mol Des"},{"issue":"2","key":"2788_CR71","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1021\/ci0255836","volume":"43","author":"T Wright","year":"2003","unstructured":"Wright T, Gillet VJ, Green DV, Pickett SD: Optimizing the size and configuration of combinatorial libraries. J Chem Inf Comput Sci 2003, 43(2):381\u2013390.","journal-title":"J Chem Inf Comput Sci"},{"issue":"6","key":"2788_CR72","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/S1093-3263(01)00150-4","volume":"20","author":"VJ Gillet","year":"2002","unstructured":"Gillet VJ, Willett P, Fleming PJ, Green DV: Designing focused libraries using MoSELECT. J Mol Graph Model 2002, 20(6):491\u2013498. 10.1016\/S1093-3263(01)00150-4","journal-title":"J Mol Graph Model"},{"key":"2788_CR73","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1385\/1-59259-802-1:335","volume":"275","author":"VJ Gillet","year":"2004","unstructured":"Gillet VJ: Designing combinatorial libraries optimized on multiple objectives. Methods Mol Biol 2004, 275: 335\u2013354.","journal-title":"Methods Mol Biol"},{"issue":"23","key":"2788_CR74","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1021\/jm020919o","volume":"45","author":"O Nicolotti","year":"2002","unstructured":"Nicolotti O, Gillet VJ, Fleming PJ, Green DV: Multiobjective optimization in quantitative structure-activity relationships: deriving accurate and interpretable QSARs. J Med Chem 2002, 45(23):5069\u20135080. 10.1021\/jm020919o","journal-title":"J Med Chem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-58\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T06:08:21Z","timestamp":1548223701000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-58"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,11]]},"references-count":74,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2788"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-58","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,2,11]]},"article-number":"58"}}