(Q47567557)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

title

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge (English)

1 reference

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24 March 2020

3

1 reference

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24 March 2020

Juyong Lee

1

1 reference

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24 March 2020

Gerhard König

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

Jing Huang

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

7

Minkyung Baek

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

8

Chaok Seok

1 reference

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24 March 2020

author name string

Florentina Tofoleanu

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

Ana Damjanović

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

Bernard R Brooks

9

1 reference

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24 March 2020

publication date

27 September 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

24 March 2020

published in

1 reference

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24 March 2020

volume

31

1 reference

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24 March 2020

issue

1

1 reference

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24 March 2020

page(s)

71-85

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

24 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Computational scheme for pH-dependent binding free energy calculation with explicit solvent

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Acyclic cucurbit[n]uril-type molecular containers: influence of glycoluril oligomer length on their function as solubilizing agents.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Blind prediction of solvation free energies from the SAMPL4 challenge.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Blind prediction of HIV integrase binding from the SAMPL4 challenge

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

The Movable Type Method Applied to Protein-Ligand Binding

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Computational methods in drug discovery

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Software and resources for computational medicinal chemistry

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Benzobis(imidazolium)-cucurbit[8]uril complexes for binding and sensing aromatic compounds in aqueous solution.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

CHARMM: the biomolecular simulation program

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Accurate reproduction of 161 small-molecule complex crystal structures using the EUDOC program: expanding the use of EUDOC to supramolecular chemistry

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

A semiempirical free energy force field with charge-based desolvation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Canonical dynamics: Equilibrium phase-space distributions

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

GalaxyDock2: protein-ligand docking using beta-complex and global optimization

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Modularity optimization by conformational space annealing.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

LigDockCSA: protein-ligand docking using conformational space annealing.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Acyclic cucurbit[n]uril congeners are high affinity hosts

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Cucurbituril homologues and derivatives: new opportunities in supramolecular chemistry

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

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

14 August 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

A fragment-based approach to the SAMPL3 Challenge

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5241186

Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field

2 November 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

Avoiding the van der Waals endpoint problem using serial atomic insertion

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

Unorthodox uses of Bennett's acceptance ratio method

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-016-9968-2

Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method

21 January 2018

1 reference

12 December 2020

Blind Prediction of Binding Affinities for Charged Supramolecular Host–Guest Systems: Achievements and Shortcomings of DFT-D3

1 reference

12 December 2020

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

1 reference

12 December 2020

Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics

1 reference

12 December 2020

The SAMPL3 blind prediction challenge: transfer energy overview

1 reference

12 December 2020

Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge

1 reference

12 December 2020

Cucurbituril-Based Molecular Recognition

1 reference

12 December 2020

10.1007/S10822-016-9968-2

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27677749%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/LeeTPKHDBSB17

24 March 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:27677749%20AND%20SRC:MED&resulttype=core&format=json

24 March 2020

PubMed publication ID

27677749

1 reference