PMID- 33769814
OWN - NLM
STAT- MEDLINE
DCOM- 20210720
LR  - 20220414
IS  - 1549-9626 (Electronic)
IS  - 1549-9618 (Print)
IS  - 1549-9618 (Linking)
VI  - 17
IP  - 4
DP  - 2021 Apr 13
TI  - Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.
PG  - 2323-2341
LID - 10.1021/acs.jctc.0c01286 [doi]
AB  - 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 
      nonlinear and linearized versions of 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 
      electrostatics 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 
      adaptive Poisson-Boltzmann solver (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 0.58 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 
      opens the door to their use for folding and design applications.
FAU - Corrigan, Rae A
AU  - Corrigan RA
AUID- ORCID: 0000-0003-3628-9347
AD  - Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, 
      Iowa 52242, United States.
FAU - Qi, Guowei
AU  - Qi G
AD  - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United 
      States.
FAU - Thiel, Andrew C
AU  - Thiel AC
AD  - Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, 
      Iowa 52242, United States.
FAU - Lynn, Jack R
AU  - Lynn JR
AD  - Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, 
      Iowa 52242, United States.
FAU - Walker, Brandon D
AU  - Walker BD
AD  - Department of Biomedical Engineering, University of Texas in Austin, Austin, 
      Texas 78712, United States.
FAU - Casavant, Thomas L
AU  - Casavant TL
AD  - Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, 
      Iowa 52242, United States.
FAU - Lagardere, Louis
AU  - Lagardere L
AD  - Department of Chemistry, Sorbonne Universite, F-75005 Paris, France.
FAU - Piquemal, Jean-Philip
AU  - Piquemal JP
AUID- ORCID: 0000-0001-6615-9426
AD  - Department of Chemistry, Sorbonne Universite, F-75005 Paris, France.
FAU - Ponder, Jay W
AU  - Ponder JW
AUID- ORCID: 0000-0001-5450-9230
AD  - Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 
      63130, United States.
FAU - Ren, Pengyu
AU  - Ren P
AUID- ORCID: 0000-0002-5613-1910
AD  - Department of Biomedical Engineering, University of Texas in Austin, Austin, 
      Texas 78712, United States.
FAU - Schnieders, Michael J
AU  - Schnieders MJ
AUID- ORCID: 0000-0003-1260-4592
AD  - Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, 
      Iowa 52242, United States.
AD  - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United 
      States.
LA  - eng
GR  - R01 DC012049/DC/NIDCD NIH HHS/United States
GR  - R01 DK110023/DK/NIDDK NIH HHS/United States
GR  - R01 GM106137/GM/NIGMS NIH HHS/United States
GR  - R01 GM114237/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20210326
PL  - United States
TA  - J Chem Theory Comput
JT  - Journal of chemical theory and computation
JID - 101232704
RN  - 0 (Ligands)
RN  - 0 (Proteins)
RN  - 0 (Solvents)
SB  - IM
MH  - Ligands
MH  - *Models, Chemical
MH  - Proteins/*chemistry
MH  - Solvents/chemistry
MH  - Static Electricity
PMC - PMC8126468
MID - NIHMS1694425
EDAT- 2021/03/27 06:00
MHDA- 2021/07/21 06:00
PMCR- 2022/04/13
CRDT- 2021/03/26 17:12
PHST- 2021/03/27 06:00 [pubmed]
PHST- 2021/07/21 06:00 [medline]
PHST- 2021/03/26 17:12 [entrez]
PHST- 2022/04/13 00:00 [pmc-release]
AID - 10.1021/acs.jctc.0c01286 [doi]
PST - ppublish
SO  - J Chem Theory Comput. 2021 Apr 13;17(4):2323-2341. doi: 10.1021/acs.jctc.0c01286. 
      Epub 2021 Mar 26.