Modeling aqueous solvation with semi-explicit assembly (Q34602658)

3 August 2017

title

Modeling aqueous solvation with semi-explicit assembly (English)

1 reference

3 August 2017

3

Ken A Dill

1 reference

3 August 2017

2

Charles W Kehoe

1 reference

3 August 2017

author name string

Christopher J Fennell

series ordinal

1

1 reference

3 August 2017

language of work or name

English

0 references

publication date

7 February 2011

1 reference

Proceedings of the National Academy of Sciences of the United States of America

3 August 2017

published in

1 reference

3 August 2017

volume

108

1 reference

3 August 2017

issue

8

1 reference

3 August 2017

page(s)

3234-3239

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

3 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Oil/water transfer is partly driven by molecular shape, not just size

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Charge asymmetries in hydration of polar solutes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Automatic atom type and bond type perception in molecular mechanical calculations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Development and testing of a general amber force field

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Electrostatics of nanosystems: application to microtubules and the ribosome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

The interpretation of protein structures: Estimation of static accessibility

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Dipolar correlations and the dielectric permittivity of water.

7 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Quantum mechanical continuum solvation models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Implicit nonpolar solvent models

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Towards molecular dynamics simulation of large proteins with a hydration shell at constant pressure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Analytical molecular surface calculation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Predictions of hydration free energies from all-atom molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044389

Free Energy of Ionic Hydration

26 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1017130108

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21300905

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21300905

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21300905

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1017130108

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference