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To improve accuracy of the molecular mechanics (MM) force field (FF) for protein\u2013ligand simulations, we use a protein\u2010specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO\u2010RESP method to two proteins, dodecin, and lysozyme, we found that protein\u2010specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO\u2010RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. \u00a9 2013 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.23250","type":"journal-article","created":{"date-parts":[[2013,2,19]],"date-time":"2013-02-19T18:34:27Z","timestamp":1361298867000},"page":"1251-1257","source":"Crossref","is-referenced-by-count":15,"title":["Protein\u2010specific force field derived from the fragment molecular orbital method can improve protein\u2013ligand binding interactions"],"prefix":"10.1002","volume":"34","author":[{"given":"Le","family":"Chang","sequence":"first","affiliation":[]},{"given":"Takeshi","family":"Ishikawa","sequence":"additional","affiliation":[]},{"given":"Kazuo","family":"Kuwata","sequence":"additional","affiliation":[]},{"given":"Shoji","family":"Takada","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2013,2,19]]},"reference":[{"key":"e_1_2_7_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd1549"},{"key":"e_1_2_7_2_2","doi-asserted-by":"crossref","unstructured":"P.Ferrara H.Gohlke D. 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