ArticleJournal of chemical theory and computation2016
Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Flexible, nonfused sulfone functionalized polymer with enhanced active site access for photocatalytic sacrificial hydrogen evolution.Science advances · 2025Article
- How well do various QM-derived net atomic charges reproduce the electrostatic potential surrounding a material across multiple geometric conformations?RSC advances · 2025Article
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation.The journal of physical chemistry. B · 2024Article
- System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids?Journal of chemical theory and computation · 2023Article
- Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions.Journal of chemical theory and computation · 2023Article
- Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.Journal of chemical information and modeling · 2022Article
- Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set.Journal of chemical theory and computation · 2022Article
- Better force fields start with better data: A data set of cation dipeptide interactions.Scientific data · 2022Article
- Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.Journal of chemical theory and computation · 2022Article
- Molecular Dynamics Simulation of Association Processes in Aqueous Solutions of Maleate Salts of Drug-like Compounds: The Role of Counterion.International journal of molecular sciences · 2022Article
- Improving 1-propanol force field: a new methodology.Journal of molecular modeling · 2022Article
- New Force-Field for Organosilicon Molecules in the Liquid Phase.ACS physical chemistry Au · 2021Article
- DL_FFLUX: A Parallel, Quantum Chemical Topology Force Field.Journal of chemical theory and computation · 2021Article
- Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds.Physical chemistry chemical physics : PCCP · 2021Article
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Authors and funding
5 authors.
Funding
Abstract
Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.
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