OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

By Edward D Harder, Wolfgang Damm, J. Maple, Chuanjie Wu, Mark Reboul, Jin Yu Xiang, Lingle Wang, Dmitry Lupyan, Markus K. Dahlgren, Jennifer L. Knight and 6 more. Journal of Chemical Theory and Computation, 2016

2,754 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Physical and Theoretical Chemistry

View Paper: https://www.semanticscholar.org/paper/f89ab690456935fc3a1f32111c7f28a931b24b10

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In Computational Theory and Mathematics

1. Rodrigo Vargas Honorato
2. Tatu Pantsar
3. Alexandre M. J. J. Bonvin
4. Antti Poso
5. David L. Mobley
6. Justin A. Lemkul

In Molecular Biology

1. David L. Mobley
2. Justin A. Lemkul
3. Rodrigo Vargas Honorato
4. Tatu Pantsar
5. Alexandre M. J. J. Bonvin
6. John D. Chodera
7. Antti Poso
8. Gregg T. Beckham

In Physical and Theoretical Chemistry

1. Alexandre M. J. J. Bonvin
2. David L. Mobley
3. Justin A. Lemkul

Citations in the corpus

• Characterization and engineering of a plastic-degrading aromatic polyesterase (2018, methodology): “PET tetramer structures (capped at both ends with ethanol groups) were prepared and energetically minimized using the Schrödinger LigPrep module according to the OPLS3 force field (21).”
• From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0] (2019, methodology): “Examples include the modeling of the σ-hole on halogens in the OPLS3 [69] and CGenFF [83] parameter sets, lone pairs on sulfur atoms in OPLS-AA and OPLS/CM5 [84], in modeling hydrogen-bond acceptors in the Drude polarizable force field [85, 86], and in repartitioning hydrogen masses onto heavier ato”
• Class I histone deacetylases (HDAC1–3) are histone lysine delactylases (2021, methodology): “Molecular docking Molecular modeling was performed with modules from the Schrödinger Small Molecule Drug Discovery Suite (Maestro), release 2018–3, using the OPLS3 force field for parameterization (80).”
• 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]).”
• Molecular dynamics simulation for all (2018, neutral): “Which force field to use? The most common choices are various versions of AMBER, CHARMM, and OPLS (Abraham et al., 2015; Harder et al., 2016; Huang et al., 2017; Robustelli et al., 2018).”
• 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]).”
• Binding Affinity via Docking: Fact and Fiction (2018, methodology): “As indirect proof of how precise these equations are, even the latest parametrization of the OPLS (Optimized Potentials for Liquid Simulations) force field family, OPLS3 [28], utilizes the formerly developed Lennard-Jones parameters.”
• Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development (2020, methodology): “Desmond together with the OPLS3 force field [25] was employed to simulate SIRT1 and SIRT3 in complex with either NAD+ or NADH and an acetyl-lysine substrate for 250–500 ns [94].”