{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T08:43:11Z","timestamp":1762504991255},"reference-count":32,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3264,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1995,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Understanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER\u2010type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. \u00a9 1995 John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540161004","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:06:56Z","timestamp":1104628016000},"page":"1210-1226","source":"Crossref","is-referenced-by-count":96,"title":["Flexible ligand docking without parameter adjustment across four ligand\u2013receptor complexes"],"prefix":"10.1002","volume":"16","author":[{"given":"Kevin P.","family":"Clark","sequence":"first","affiliation":[]},{"family":"Ajay","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.257.5073.1078"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540060510"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm00145a002"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130412"},{"key":"e_1_2_1_6_2","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/BF00126743","volume":"8","author":"Bohm H. J.","year":"1994","journal-title":"Comp.\u2010Aid. Mol. Design"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(91)90859-5"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80038-5"},{"key":"e_1_2_1_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540060504"},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340080302"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340130304"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130608"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1021\/ar00041a001"},{"key":"e_1_2_1_14_2","volume-title":"Genetic Algorithms in Search, Optimization, and Machine Learning","author":"Goldberg D. E.","year":"1989"},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00315a051"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540070216"},{"key":"e_1_2_1_17_2","unstructured":"Molecular Modeling System SYBYL Version 5.4 Tripos Associates Inc. St. Louis MO J. Comp. Chem.(1991)."},{"key":"e_1_2_1_18_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889883010985"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.6879170"},{"key":"e_1_2_1_20_2","volume-title":"Adaptation in Natural and Artificial Systems","author":"Holland J. H.","year":"1975"},{"key":"e_1_2_1_21_2","volume-title":"Tech. Rep. CS92\u2010249","author":"Schraudolph Nicol N.","year":"1990"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(77)80200-3"},{"key":"e_1_2_1_23_2","first-page":"107","volume-title":"Crystallographic Databases: Information Content, Software Systems, Scientific Applications","author":"Abola E. E.","year":"1987"},{"key":"e_1_2_1_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.3057628"},{"key":"e_1_2_1_25_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.83.20.7568"},{"key":"e_1_2_1_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)33497-5"},{"key":"e_1_2_1_27_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00329a038"},{"key":"e_1_2_1_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340170305"},{"key":"e_1_2_1_29_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00119865"},{"key":"e_1_2_1_30_2","unstructured":"AjayandK. P.Clark Possible pitfalls with computational docking strategies: Methotrexate docking to dihydrofolate reductase work in progress."},{"key":"e_1_2_1_31_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560010204"},{"key":"e_1_2_1_32_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00172a038"},{"key":"e_1_2_1_33_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130213"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.540161004","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.540161004","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,26]],"date-time":"2023-10-26T19:48:12Z","timestamp":1698349692000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.540161004"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[1995,10]]},"references-count":32,"journal-issue":{"issue":"10","published-print":{"date-parts":[[1995,10]]}},"alternative-id":["10.1002\/jcc.540161004"],"URL":"https:\/\/doi.org\/10.1002\/jcc.540161004","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[1995,10]]}}}