{"title":"结合经典分子对接与自洽电荷密度功能紧密结合计算,实现配体结合结构的高效、高质量预测","authors":"Amar Y. Al-Ansi, Haorui Lu, Zijing Lin","doi":"10.1177/17475198221101999","DOIUrl":null,"url":null,"abstract":"To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.","PeriodicalId":15318,"journal":{"name":"Journal of Chemical Research-s","volume":"4 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure\",\"authors\":\"Amar Y. Al-Ansi, Haorui Lu, Zijing Lin\",\"doi\":\"10.1177/17475198221101999\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.\",\"PeriodicalId\":15318,\"journal\":{\"name\":\"Journal of Chemical Research-s\",\"volume\":\"4 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2022-03-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Research-s\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1177/17475198221101999\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Research-s","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1177/17475198221101999","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure
To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.
期刊介绍:
The Journal of Chemical Research is a peer reviewed journal that publishes full-length review and research papers in all branches of experimental chemistry. The journal fills a niche by also publishing short papers, a format which favours particular types of work, e.g. the scope of new reagents or methodology, and the elucidation of the structure of novel compounds. Though welcome, short papers should not result in fragmentation of publication, they should describe a completed piece of work. The Journal is not intended as a vehicle for preliminary publications. The work must meet all the normal criteria for acceptance as regards scientific standards. Papers that contain extensive biological results or material relating to other areas of science may be diverted to more appropriate specialist journals. Areas of coverage include: Organic Chemistry; Inorganic Chemistry; Materials Chemistry; Crystallography; Computational Chemistry.