(Q39379522)

English

The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method (English)

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

0 references

author name string

Jian Yin

1

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

Niel M Henriksen

2

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

David R Slochower

3

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

Michael K Gilson

4

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

publication date

16 September 2016

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

Journal of Computer - Aided Molecular Design

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

31

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

1

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

133-145

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

https://scigraph.springernature.com/pub.10.1007/s10822-016-9970-8

0 references

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Overview of the SAMPL5 host-guest challenge: Are we doing better?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Building Water Models: A Different Approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Acyclic cucurbit[n]uril-type molecular containers: influence of aromatic walls on their function as solubilizing excipients for insoluble drugs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Molecular containers assembled through the hydrophobic effect

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Blind prediction of solvation free energies from the SAMPL4 challenge.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

The SAMPL4 host-guest blind prediction challenge: an overview.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Binding of cyclic carboxylates to octa-acid deep-cavity cavitand

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Molecular dynamics simulations and drug discovery

1 reference

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17 June 2018

Poly(β-cyclodextrin)/curcumin self-assembly: a novel approach to improve curcumin delivery and its therapeutic efficacy in prostate cancer cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Computations of standard binding free energies with molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Statistically optimal analysis of samples from multiple equilibrium states

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Development and testing of a general amber force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

The statistical-thermodynamic basis for computation of binding affinities: a critical review

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

17 June 2018

The SAMPL2 blind prediction challenge: introduction and overview.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241238

21 August 2018

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9970-8

21 January 2018

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9970-8

21 January 2018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9970-8

21 January 2018

Molecular dynamics with coupling to an external bath

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9970-8

21 January 2018

Summary for Policymakers

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9970-8

21 January 2018

Guest-mediated switching of the assembly state of a water-soluble deep-cavity cavitand

1 reference

https://pubmed.ncbi.nlm.nih.gov/27638809

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

1 reference

https://pubmed.ncbi.nlm.nih.gov/27638809

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nonmonotonic assembly of a deep-cavity cavitand

1 reference

https://pubmed.ncbi.nlm.nih.gov/27638809

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Isotropic periodic sum: a method for the calculation of long-range interactions.

1 reference

https://pubmed.ncbi.nlm.nih.gov/27638809

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1007/S10822-016-9970-8

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

DBLP publication ID

journals/jcamd/YinHSG17

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

8 January 2018

http://europepmc.org/abstract/PMC/5241238

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