(Q27860745)

5

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Thomas E. Cheatham, III

2

object named as

Thomas E Cheatham

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author name string

David A Case

1

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Tom Darden

3

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Holger Gohlke

4

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Kenneth M Merz

6

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Alexey Onufriev

7

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Carlos Simmerling

8

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Bing Wang

9

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Robert J Woods

Journal of Computational Chemistry

10

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publication date

December 2005

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published in

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volume

26

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issue

16

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page(s)

1668-88

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cites work

Optimization by Simulated Annealing

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Solvent interactions determine carbohydrate conformation

20 March 2017

1 reference

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VMD: visual molecular dynamics

20 March 2017

1 reference

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Effective Born radii in the generalized Born approximation: the importance of being perfect

20 March 2017

1 reference

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Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Development and testing of a general amber force field

7 April 2017

1 reference

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Exploring protein native states and large-scale conformational changes with a modified generalized born model

7 April 2017

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

7 April 2017

1 reference

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Essential dynamics of proteins

7 April 2017

1 reference

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Classical electrostatics in biology and chemistry

7 April 2017

1 reference

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Solvated ensemble averaging in the calculation of partial atomic charges

7 April 2017

1 reference

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Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

29 September 2017

1 reference

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MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

29 September 2017

1 reference

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

29 September 2017

1 reference

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Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

29 September 2017

1 reference

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Force fields for protein simulations

29 September 2017

1 reference

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On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Combined quantum and molecular mechanics calculations on metalloproteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Generalized-ensemble algorithms for molecular simulations of biopolymers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Generalized born models of macromolecular solvation effects

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Translational and rotational diffusion of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Are there non-trivial dynamic cross-correlations in proteins?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Collective variable description of native protein dynamics

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Incorporating variable dielectric environments into the generalized Born model

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Implicit solvation based on generalized Born theory in different dielectric environments

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

All-atom generalized-ensemble simulations of small proteins.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Ion solvation thermodynamics from simulation with a polarizable force field

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Dynamic and structural analysis of isotropically distributed molecular ensembles

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1989667

Reorientational Eigenmode Dynamics: A Combined MD/NMR Relaxation Analysis Method for Flexible Parts in Globular Proteins

27 November 2018

1 reference

12 December 2020

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

1 reference

12 December 2020

General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation

1 reference

12 December 2020

Generation of accurate protein loop conformations through low-barrier molecular dynamics

1 reference

12 December 2020

Poisson–Boltzmann Methods for Biomolecular Electrostatics

1 reference

12 December 2020

Computer Simulation of the Static Dielectric Constant of Systems with Permanent Electric Dipoles

1 reference

12 December 2020

Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.20290

1 reference

journals/jcc/CaseCDGLMOSWW05

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

16200636

1 reference