(Q33819349)

29 July 2017

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber (English)

1 reference

29 July 2017

5

David A Case

0 references

author name string

Tyler Luchko

1

1 reference

29 July 2017

Sergey Gusarov

2

1 reference

29 July 2017

Daniel R Roe

3

1 reference

29 July 2017

Carlos Simmerling

4

1 reference

29 July 2017

David A Case

5

1 reference

29 July 2017

Jack Tuszynski

6

1 reference

29 July 2017

Andriy Kovalenko

7

1 reference

29 July 2017

1 March 2010

1 reference

Journal of Chemical Theory and Computation

29 July 2017

1 reference

29 July 2017

6

1 reference

29 July 2017

3

1 reference

29 July 2017

607-624

1 reference

Generalized Born model with a simple, robust molecular volume correction

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

A molecular site-site integral equation that yields the dielectric constant

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Microtubule stability studied by three-dimensional molecular theory of solvation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

The Amber biomolecular simulation programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

A molecular dynamics simulation study of segment B1 of protein G.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Localization of bound water in the solution structure of the immunoglobulin binding domain of streptococcal protein G. Evidence for solvent-induced helical distortion in solution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

An interaction site model integral equation study of molecular fluids explicitly considering the molecular orientation.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Helical rosette nanotubes with tunable stability and hierarchy.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Protein molecular dynamics with the generalized born/ACE solvent model

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2861832

Molecular basis for water-promoted supramolecular chirality inversion in helical rosette nanotubes

29 October 2018

1 reference

12 December 2020

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra

1 reference

12 December 2020

Hierarchical self-assembly of organic prolate nanospheroids from hydrophobic rosette nanotubes

1 reference

12 December 2020

Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design

1 reference

12 December 2020

Structural water drives self-assembly of organic rosette nanotubes and holds host atoms in the channel

1 reference

12 December 2020

Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers.

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT900460M

1 reference

29 July 2017

1 reference

29 July 2017

1 reference