OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.
By Katarina Roos, Chuanjie Wu, Wolfgang Damm, Mark Reboul, James M Stevenson, Chao Lu, Markus K. Dahlgren, Sayantan Mondal, Wei Chen, Lingle Wang and 3 more. Journal of Chemical Theory and Computation, 2019
1,023 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/32087d0ac1f420164ddef04ce0c6bcbebfe74e15
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Citations in the corpus
- Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0] (2021, methodology): “Schrödinger utilized the same benchmark set to assess subsequent commercial force field releases (OPLS3 [21] and OPLS3e [22]).”
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.2] (2021, methodology): “Schrödinger utilized the same benchmark set to assess subsequent commercial force field releases (OPLS3 [21] and OPLS3e [22]).”
- Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field (2023, neutral): “ΔΔEi = ΔEMM,i − ΔEQM,i = [EMM (xi) − EMM (x0,QM )] − [EQM (xi) − EQM (x0,QM )] (9) where, the relative conformer energies were calculated with respect to the QMminimum energy conformer (labeled 0th) within each molecule, through a conformer matching process.”