Generalized Born model with a simple, robust molecular volume correction (Q34287102)

1 August 2017

Generalized Born model with a simple, robust molecular volume correction (English)

1 reference

1 August 2017

0 references

3

J Andrew McCammon

1 reference

1 August 2017

John Mongan

1

1 reference

1 August 2017

Carlos Simmerling

series ordinal

2

1 reference

1 August 2017

David A Case

series ordinal

4

1 reference

1 August 2017

Alexey Onufriev

series ordinal

5

1 reference

1 August 2017

1 January 2007

1 reference

Journal of Chemical Theory and Computation

1 August 2017

1 reference

1 August 2017

3

1 reference

1 August 2017

1

1 reference

1 August 2017

156-169

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

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Improving implicit solvent simulations: a Poisson-centric view

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Generalized born models of macromolecular solvation effects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Calculations of proton-binding thermodynamics in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Classical electrostatics in biology and chemistry

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

The interpretation of protein structures: Estimation of static accessibility

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Limitations of atom-centered dielectric functions in implicit solvent models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Incorporating variable dielectric environments into the generalized Born model

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Generalized born model with a simple smoothing function.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Structural details, pathways, and energetics of unfolding apomyoglobin

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Protein molecular dynamics with the generalized born/ACE solvent model

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2975579

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21072141

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Potentials of mean force between ionizable amino acid side chains in water

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21072141

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT600085E

1 reference

1 August 2017

1 reference

1 August 2017

1 reference