Home
Random
Nearby
Log in
Settings
Donate
About Wikidata
Disclaimers
Search
(Q33874112)
Watch
English
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.
scientific article
In more languages
edit
Statements
instance of
scholarly article
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
title
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
(English)
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
main subject
force field
0 references
author
Pengyu Ren
series ordinal
5
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
Jayvee R Abella
series ordinal
1
object named as
Jayvee R Abella
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
author name string
Sara Y Cheng
series ordinal
2
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
Qiantao Wang
series ordinal
3
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
Wei Yang
series ordinal
4
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
publication date
9 May 2014
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
published in
Journal of Chemical Theory and Computation
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
volume
10
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
issue
7
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
page(s)
2792-2801
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
cites work
A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
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
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Automation of AMOEBA polarizable force field parameterization for small molecules
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Multipole electrostatics in hydration free energy calculations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Current status of the AMOEBA polarizable force field
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Statistically optimal analysis of samples from multiple equilibrium states
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Calculation of protein-ligand binding free energy by using a polarizable potential
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Canonical sampling through velocity rescaling
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
The many roles of computation in drug discovery
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Escaping free-energy minima
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
5 July 2018
Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Ion solvation thermodynamics from simulation with a polarizable force field
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4089918
retrieved
29 October 2018
Quasichemical and structural analysis of polarizable anion hydration
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25018674
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25018674
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25018674
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1021/CT500202Q
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
PMC publication ID
4089918
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
PubMed publication ID
25018674
1 reference
stated in
Europe PubMed Central
PMC publication ID
4089918
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25018674%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 March 2020
ResearchGate publication ID
263898856
0 references
Sitelinks
Wikipedia
(0 entries)
edit
Wikibooks
(0 entries)
edit
Wikinews
(0 entries)
edit
Wikiquote
(0 entries)
edit
Wikisource
(0 entries)
edit
Wikiversity
(0 entries)
edit
Wikivoyage
(0 entries)
edit
Wiktionary
(0 entries)
edit
Multilingual sites
(0 entries)
edit