دورية أكاديمية
أعرض في EDS

Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters.

التفاصيل البيبلوغرافية
العنوان: Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters.
المؤلفون: Ehrman JN; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA., Lim VT; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA., Bannan CC; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA., Thi N; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA., Kyu DY; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA., Mobley DL; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. dmobley@mobleylab.org.; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA. dmobley@mobleylab.org.
المصدر: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2021 Mar; Vol. 35 (3), pp. 271-284. Date of Electronic Publication: 2021 Jan 28.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Springer Country of Publication: Netherlands NLM ID: 8710425 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-4951 (Electronic) Linking ISSN: 0920654X NLM ISO Abbreviation: J Comput Aided Mol Des Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Springer
Original Publication: Leiden, The Netherlands : ESCOM, [c1987-
مواضيع طبية MeSH: Aza Compounds/*chemistry , Organic Chemicals/*chemistry, Databases, Chemical ; Models, Molecular ; Molecular Conformation ; Physical Phenomena ; Quantum Theory ; Software ; Structure-Activity Relationship ; Thermodynamics
مستخلص: Many molecular simulation methods use force fields to help model and simulate molecules and their behavior in various environments. Force fields are sets of functions and parameters used to calculate the potential energy of a chemical system as a function of the atomic coordinates. Despite the widespread use of force fields, their inadequacies are often thought to contribute to systematic errors in molecular simulations. Furthermore, different force fields tend to give varying results on the same systems with the same simulation settings. Here, we present a pipeline for comparing the geometries of small molecule conformers. We aimed to identify molecules or chemistries that are particularly informative for future force field development because they display inconsistencies between force fields. We applied our pipeline to a subset of the eMolecules database, and highlighted molecules that appear to be parameterized inconsistently across different force fields. We then identified over-represented functional groups in these molecule sets. The molecules and moieties identified by this pipeline may be particularly helpful for future force field parameterization.
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معلومات مُعتمدة: R01 GM108889 United States GM NIGMS NIH HHS; R01 GM132386 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: Conformer comparison; Force fields; Geometry optimization; Molecular mechanics simulations; Molecular modeling
المشرفين على المادة: 0 (Aza Compounds)
0 (Organic Chemicals)
تواريخ الأحداث: Date Created: 20210128 Date Completed: 20220105 Latest Revision: 20231111
رمز التحديث: 20231111
مُعرف محوري في PubMed: PMC8162916
DOI: 10.1007/s10822-020-00367-1
PMID: 33506360
قاعدة البيانات: MEDLINE
الوصف
تدمد:1573-4951
DOI:10.1007/s10822-020-00367-1