Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms (Q34694062)

4 August 2017

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

1 reference

4 August 2017

2

1 reference

4 August 2017

Jason A Wagoner

1

1 reference

PubMed ID

16709675

4 August 2017

language of work or name

English

0 references

publication date

18 May 2006

1 reference

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

4 August 2017

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4 August 2017

103

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4 August 2017

8331-8336

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4 August 2017

22

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4 August 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Strong solute-solute dispersive interactions in a protein-ligand complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Improving implicit solvent simulations: a Poisson-centric view

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Recent advances in the development and application of implicit solvent models in biomolecule 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=1482494

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

The weighted-volume derivative of a space-filling diagram

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

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=1482494

Generalized born models of macromolecular solvation effects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Classical electrostatics in biology and chemistry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

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=1482494

Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Hydrophobic bonding and accessible surface area in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Solvation energy in protein folding and binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Hydrophobic effect in protein folding and other noncovalent processes involving proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Atomic solvation parameters applied to molecular dynamics of proteins in solution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

Coupling nonpolar and polar solvation free energies in implicit solvent models

7 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

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.0600118103

The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

A Poisson–Boltzmann dynamics method with nonperiodic boundary condition

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Calculation of molecular volumes and areas for structures of known geometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

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.0600118103

Role of solvent in determining conformational preferences of alanine dipeptide in water.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

Correlating solvation free energies and surface tensions of hydrocarbon solutes.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482494

New perspectives on hydrophobic effects

26 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600118103

On the temperature and pressure dependences of cavities in the dielectric continuum picture

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16709675

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Comparative study of generalized born models: Born radii and peptide folding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16709675

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

On the mechanism of hydrophobic association of nanoscopic solutes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16709675

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0600118103

1 reference

4 August 2017

0 references

1 reference

4 August 2017

1 reference

PubMed ID

16709675