Literature DB >> 20136072

Current status of the AMOEBA polarizable force field.

Jay W Ponder1, Chuanjie Wu, Pengyu Ren, Vijay S Pande, John D Chodera, Michael J Schnieders, Imran Haque, David L Mobley, Daniel S Lambrecht, Robert A DiStasio, Martin Head-Gordon, Gary N I Clark, Margaret E Johnson, Teresa Head-Gordon.   

Abstract

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the <span class="Chemical">alanine tetrapeptide and isomers of <span class="Chemical">water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20136072      PMCID: PMC2918242          DOI: 10.1021/jp910674d

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  48 in total

1.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

3.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

4.  Distributed Multipole Analysis:  Stability for Large Basis Sets.

Authors:  Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

5.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal:  Proteins       Date:  2006-11-15

6.  Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

Authors:  Michael R Shirts; David L Mobley; John D Chodera; Vijay S Pande
Journal:  J Phys Chem B       Date:  2007-10-19       Impact factor: 2.991

7.  Version 1.2 of the Crystallography and NMR system.

Authors:  Axel T Brunger
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

8.  Hydration water dynamics near biological interfaces.

Authors:  Margaret E Johnson; Cecile Malardier-Jugroot; Rajesh K Murarka; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2009-04-02       Impact factor: 2.991

9.  A Resolution-Of-The-Identity Implementation of the Local Triatomics-In-Molecules Model for Second-Order Møller-Plesset Perturbation Theory with Application to Alanine Tetrapeptide Conformational Energies.

Authors:  Robert A DiStasio; Yousung Jung; Martin Head-Gordon
Journal:  J Chem Theory Comput       Date:  2005-09       Impact factor: 6.006

10.  Efficient Simulation Method for Polarizable Protein Force Fields:  Application to the Simulation of BPTI in Liquid Water.

Authors:  Edward Harder; Byungchan Kim; Richard A Friesner; B J Berne
Journal:  J Chem Theory Comput       Date:  2005-01       Impact factor: 6.006

View more
  272 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

2.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

3.  Molecular simulation methods in drug discovery: a prospective outlook.

Authors:  Xavier Barril; F Javier Luque
Journal:  J Comput Aided Mol Des       Date:  2011-12-08       Impact factor: 3.686

4.  An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling.

Authors:  Parin Sripakdeevong; Wipapat Kladwang; Rhiju Das
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-05       Impact factor: 11.205

5.  Natural polarizability and flexibility via explicit valency: the case of water.

Authors:  Seyit Kale; Judith Herzfeld
Journal:  J Chem Phys       Date:  2012-02-28       Impact factor: 3.488

Review 6.  Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.

Authors:  Pierre Tuffery; Philippe Derreumaux
Journal:  J R Soc Interface       Date:  2011-10-12       Impact factor: 4.118

Review 7.  Taming the complexity of protein folding.

Authors:  Gregory R Bowman; Vincent A Voelz; Vijay S Pande
Journal:  Curr Opin Struct Biol       Date:  2011-02       Impact factor: 6.809

8.  Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins.

Authors:  Zhifeng Jing; Chengwen Liu; Rui Qi; Pengyu Ren
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-23       Impact factor: 11.205

9.  The unsolved "solved-problem" of protein folding.

Authors:  B Montgomery Pettitt
Journal:  J Biomol Struct Dyn       Date:  2013-02-05

10.  Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

Authors:  Jing Huang; Justin A Lemkul; Peter K Eastman; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-05-04       Impact factor: 3.376

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.