Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations (Q39901298)

15 September 2017

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

1 reference

15 September 2017

Michael R Shirts

1 reference

15 September 2017

David L Mobley

0 references

Ken A Dill

1 reference

15 September 2017

Christopher I Bayly

1 reference

PMC publication ID

2701304

15 September 2017

Matthew D Cooper

series ordinal

1 reference

15 September 2017

1 February 2009

1 reference

Journal of Chemical Theory and Computation

15 September 2017

1 reference

15 September 2017

1 reference

15 September 2017

1 reference

15 September 2017

350-358

1 reference

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

15 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Empirical correlation between hydrophobic free energy and aqueous cavity surface area

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

GROMACS: fast, flexible, and free

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Development and testing of a general amber force field

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Charge asymmetries in hydration of polar solutes.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Treating entropy and conformational changes in implicit solvent simulations of small molecules

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Hydrophobic bonding and accessible surface area in proteins

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Implicit nonpolar solvent models

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Surfaces affect ion pairing

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2701304

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

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20150953

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20150953

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT800409D

1 reference

15 September 2017

1 reference

PMC publication ID

2701304

15 September 2017

PubMed publication ID

20150953

1 reference

PMC publication ID

2701304