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COMPASS II:聚合物和类药物分子数据库的扩展覆盖范围。

COMPASS II: extended coverage for polymer and drug-like molecule databases.

作者信息

Sun Huai, Jin Zhao, Yang Chunwei, Akkermans Reinier L C, Robertson Struan H, Spenley Neil A, Miller Simon, Todd Stephen M

机构信息

School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.

Dassault Systèmes BIOVIA, 334 Cambridge Science Park, Cambridge, CB4 0WN, UK.

出版信息

J Mol Model. 2016 Feb;22(2):47. doi: 10.1007/s00894-016-2909-0. Epub 2016 Jan 27.

Abstract

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338-7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

摘要

COMPASS II力场是通过将COMPASS力场(《物理化学杂志B》102(38):7338 - 7364, 1998)的覆盖范围扩展到常见数据库中的聚合物和类药物分子而开发的。使用一种碎片化方法系统地构建展示这些数据库中关键官能团的小分子,从而有效地获得了适用于数据库化合物的参数。基于与COMPASS力场开发中使用的相同参数化范式,通过对价参数的量子力学数据拟合以及对非键参数的实验液体和晶体数据拟合相结合,推导出了新的参数。为了保持原始COMPASS参数的质量,使用并更新了一个质量保证套件,以确保额外的原子类型和参数不会干扰现有的参数。针对分子性质、液体和晶体密度以及焓的验证表明,COMPASS的质量得以保持,并且对于额外的覆盖范围也实现了相同的预测质量。

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