Literature DB >> 30768902

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.

Katarina Roos1,2, Chuanjie Wu3, Wolfgang Damm3, Mark Reboul3, James M Stevenson3, Chao Lu3, Markus K Dahlgren3, Sayan Mondal3, Wei Chen3, Lingle Wang3, Robert Abel3, Richard A Friesner1, Edward D Harder3.   

Abstract

Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by addressing limitations in chemotype transferability. OPLS3e accomplishes this by incorporating new parameter types that recognize moieties with greater chemical specificity and integrating an on-the-fly parametrization approach to the assignment of partial charges. As a consequence, OPLS3e leads to greater accuracy against performance benchmarks that assess small molecule conformational propensities, solvation, and protein-ligand binding.

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Year:  2019        PMID: 30768902     DOI: 10.1021/acs.jctc.8b01026

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  158 in total

1.  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking.

Authors:  Hahnbeom Park; Guangfeng Zhou; Minkyung Baek; David Baker; Frank DiMaio
Journal:  J Chem Theory Comput       Date:  2021-02-12       Impact factor: 6.006

2.  Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

3.  Debio-0932, a second generation oral Hsp90 inhibitor, induces apoptosis in MCF-7 and MDA-MB-231 cell lines.

Authors:  Aykut Özgür; Altan Kara; Nazan Gökşen Tosun; Şaban Tekin; İsa Gökçe
Journal:  Mol Biol Rep       Date:  2021-05-17       Impact factor: 2.316

4.  Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations.

Authors:  Jianxin Duan; Dmitry Lupyan; Lingle Wang
Journal:  Biophys J       Date:  2020-05-29       Impact factor: 4.033

5.  NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G.

Authors:  Sohini Chakraborti; Neha Khare; Sumana Das; Saqib Kidwai; Rania Bouzeyen; Tannu Priya Gosain; Assirbad Behura; Chhuttan Lal Meena; Rohan Dhiman; Makram Essafi; Avinash Bajaj; Deepak Kumar Saini; Narayanaswamy Srinivasan; Dinesh Mahajan; Ramandeep Singh
Journal:  Antimicrob Agents Chemother       Date:  2019-08-23       Impact factor: 5.191

6.  Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Authors:  David R Slochower; Niel M Henriksen; Lee-Ping Wang; John D Chodera; David L Mobley; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2019-10-25       Impact factor: 6.006

7.  Two-step reaction mechanism reveals new antioxidant capability of cysteine disulfides against hydroxyl radical attack.

Authors:  Sarju Adhikari; Ramon Crehuet; Josep M Anglada; Joseph S Francisco; Yu Xia
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-17       Impact factor: 11.205

8.  Size-selective Catalytic Polymer Acylation with a Molecular Tetrahedron.

Authors:  Mona Sharafi; Kyle T McKay; Monika Ivancic; Dillon R McCarthy; Natavan Dudkina; Kyle E Murphy; Sinu C Rajappan; Joseph P Campbell; Yuxiang Shen; Appala Raju Badireddy; Jianing Li; Severin T Schneebeli
Journal:  Chem       Date:  2020-06-11       Impact factor: 22.804

9.  Conformational Changes in Tyrosine 11 of Neurotensin Are Required to Activate the Neurotensin Receptor 1.

Authors:  Fabian Bumbak; Trayder Thomas; Billy J Noonan-Williams; Tasneem M Vaid; Fei Yan; Alice R Whitehead; Shoni Bruell; Martina Kocan; Xuan Tan; Margaret A Johnson; Ross A D Bathgate; David K Chalmers; Paul R Gooley; Daniel J Scott
Journal:  ACS Pharmacol Transl Sci       Date:  2020-04-29

10.  GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps.

Authors:  Michael J Robertson; Gydo C P van Zundert; Kenneth Borrelli; Georgios Skiniotis
Journal:  Structure       Date:  2020-05-14       Impact factor: 5.006

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