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- W4237384091 abstract "Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>" @default.
- W4237384091 created "2022-05-12" @default.
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- W4237384091 date "2020-12-17" @default.
- W4237384091 modified "2023-10-16" @default.
- W4237384091 title "Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field" @default.
- W4237384091 doi "https://doi.org/10.26434/chemrxiv.13381046.v1" @default.
- W4237384091 hasPublicationYear "2020" @default.
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