FreeSolv: a database of experimental and calculated hydration free energies, with input files (Q28655211)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

author name string

J Peter Guthrie

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

8 June 2020

language of work or name

English

0 references

publication date

July 2014

0 references

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

volume

28

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

page(s)

711-720

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

Biomolecular electrostatics and solvation: a computational perspective

8 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

ACPYPE - AnteChamber PYthon Parser interfacE

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

GROMACS: fast, flexible, and free

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

The Amber biomolecular simulation programs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Development and testing of a general amber force field

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Automatic atom type and bond type perception in molecular mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Blind prediction of solvation free energies from the SAMPL4 challenge.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

An introduction to best practices in free energy calculations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Alchemical prediction of hydration free energies for SAMPL.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Alchemical free energy methods for drug discovery: progress and challenges

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Modeling aqueous solvation with semi-explicit assembly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

The AGBNP2 Implicit Solvation Model.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Current status of the AMOEBA polarizable force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Basic ingredients of free energy calculations: a review

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Ion pairing in molecular simulations of aqueous alkali halide solutions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Charge asymmetries in hydration of polar solutes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

3 June 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

Surfaces affect ion pairing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

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/10.1007%2FS10822-014-9747-X

Charge hydration asymmetry: the basic principle and how to use it to test and improve water models

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

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/10.1007%2FS10822-014-9747-X

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/10.1007%2FS10822-014-9747-X

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9747-X

Optimizing solute-water van der Waals interactions to reproduce solvation free energies.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4113415

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

27 November 2018

1 reference

12 December 2020

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

1 reference

12 December 2020

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

1 reference

12 December 2020

The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization

1 reference

12 December 2020

10.1007/S10822-014-9747-X

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

DBLP publication ID

journals/jcamd/MobleyG14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

PubMed publication ID

24928188

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24928188%20AND%20SRC:MED&resulttype=core&format=json