Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies (Q37390899)

20 August 2017

Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies (English)

1 reference

20 August 2017

5

1 reference

20 August 2017

Michael D Daily

1

1 reference

20 August 2017

Jaehun Chun

series ordinal

2

1 reference

20 August 2017

Alejandro Heredia-Langner

series ordinal

3

1 reference

20 August 2017

Guowei Wei

series ordinal

4

1 reference

20 August 2017

language of work or name

English

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publication date

1 November 2013

1 reference

Journal of Chemical Physics

20 August 2017

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20 August 2017

139

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20 August 2017

20

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20 August 2017

204108

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Parameterization of a geometric flow implicit solvation model

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Variational approach for nonpolar solvation analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Differential geometry based solvation model II: Lagrangian formulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Accounting for electronic polarization in non-polarizable force fields

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Differential geometry based solvation model I: Eulerian formulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Automatic atom type and bond type perception in molecular mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Development and testing of a general amber force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Solvent-accessible surfaces of proteins and nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Solvation energy in protein folding and binding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Differential geometry based solvation model. III. Quantum formulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

On the Dielectric Boundary in Poisson-Boltzmann Calculations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Hydrophobic bonding and accessible surface area in proteins

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Internal pressure of liquids and solutions

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Implicit nonpolar solvent models

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Minimal molecular surfaces and their applications

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Coupling nonpolar and polar solvation free energies in implicit solvent models

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

Rapid atomic density methods for molecular shape characterization.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3862591

New perspectives on hydrophobic effects

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063/1.4832900

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24289345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24289345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4832900

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

24289345

1 reference