(Q30419602)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

Alchemical prediction of hydration free energies for SAMPL (English)

1 reference

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19 January 2020

1

1 reference

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19 January 2020

author name string

Shaui Liu

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

David S Cerutti

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

William C Swope

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Julia E Rice

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

publication date

24 December 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

19 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

26

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

551-562

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration

19 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Alchemical free energy methods for drug discovery: progress and challenges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Predicting absolute ligand binding free energies to a simple model site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Automatic atom type and bond type perception in molecular mechanical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

The Amber biomolecular simulation programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

Development and testing of a general amber force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

20 June 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

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%2FS10822-011-9528-8

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

The SAMPL2 blind prediction challenge: introduction and overview.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9528-8

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583515

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

26 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

An interpretation of the enhancement of the water dipole moment due to the presence of other water molecules

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1007/S10822-011-9528-8

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/MobleyLCSR12

19 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22198475%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

22198475

1 reference