(Q30360256)

21 August 2017

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units (English)

1 reference

molecular dynamics simulation

21 August 2017

0 references

0 references

4

Vijay Pande

Vijay

Pande

1 reference

21 August 2017

5

J Andrew McCammon

J. Andrew

McCammon

1 reference

21 August 2017

3

Peter Eastman

1 reference

21 August 2017

Steffen Lindert

1

1 reference

PMC publication ID

3948463

21 August 2017

Denis Bucher

series ordinal

2

1 reference

21 August 2017

15 October 2013

1 reference

Journal of Chemical Theory and Computation

21 August 2017

1 reference

21 August 2017

9

1 reference

21 August 2017

11

1 reference

21 August 2017

4684-4691

1 reference

OpenMM: A Hardware Independent Framework for Molecular Simulations

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Enhanced sampling algorithms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Systematic validation of protein force fields against experimental data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Implementation of Accelerated Molecular Dynamics in NAMD

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Atomic-level characterization of the structural dynamics of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

GPU-accelerated molecular modeling coming of age

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Improved side-chain torsion potentials for the Amber ff99SB protein force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Current status of the AMOEBA polarizable force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Improved sampling methods for molecular simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

On the application of accelerated molecular dynamics to liquid water simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

The Amber biomolecular simulation programs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Escaping free-energy minima

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Dynamics of folded proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Polarization effects and charge transfer in the KcsA potassium channel.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3948463

Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24634618

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24634618

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT400514P

1 reference

21 August 2017

1 reference

PMC publication ID

3948463

21 August 2017

PubMed publication ID

24634618

1 reference

PMC publication ID

3948463