(Q36801376)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Yang Gao

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

2

Haoyuan Chen

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

author name string

He Chen

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Michael Fitzgerald

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Peng He

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Malathi Kalyanikar

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Chuan Kao

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Beidi Lu

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Yijie Niu

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Manasi Pethe

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Jie Zhu

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Ronald M Levy

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

language of work or name

1 reference

1 March 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

1 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

volume

29

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

315-325

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1007/s10822-014-9795-2

1 March 2020

exact match

0 references

cites work

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1 reference

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

29 September 2017

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Blind prediction of HIV integrase binding from the SAMPL4 challenge

29 September 2017

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Interrogating HIV integrase for compounds that bind- a SAMPL challenge

29 September 2017

1 reference

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SAMPL4 & DOCK3.7: lessons for automated docking procedures

29 September 2017

1 reference

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

29 September 2017

1 reference

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

29 September 2017

1 reference

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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

29 September 2017

1 reference

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

29 September 2017

1 reference

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Lead optimization mapper: automating free energy calculations for lead optimization

29 September 2017

1 reference

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CSAR data set release 2012: ligands, affinities, complexes, and docking decoys

29 September 2017

1 reference

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Perspective: Alchemical free energy calculations for drug discovery

29 September 2017

1 reference

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Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

29 September 2017

1 reference

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Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase

29 September 2017

1 reference

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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

29 September 2017

1 reference

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Theory of binless multi-state free energy estimation with applications to protein-ligand binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

29 September 2017

1 reference

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Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

29 September 2017

1 reference

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Recent theoretical and computational advances for modeling protein-ligand binding affinities

29 September 2017

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Alchemical free energy methods for drug discovery: progress and challenges

29 September 2017

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Advances in all atom sampling methods for modeling protein-ligand binding affinities

29 September 2017

1 reference

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

29 September 2017

1 reference

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Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models

29 September 2017

1 reference

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The AGBNP2 Implicit Solvation Model.

29 September 2017

1 reference

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

29 September 2017

1 reference

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Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

29 September 2017

1 reference

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Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution

29 September 2017

1 reference

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Statistically optimal analysis of samples from multiple equilibrium states

29 September 2017

1 reference

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Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets

29 September 2017

1 reference

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

29 September 2017

1 reference

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Integrated Modeling Program, Applied Chemical Theory (IMPACT)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

The many roles of computation in drug discovery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Lead discovery using molecular docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Automated docking of flexible ligands: applications of AutoDock

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Let's get honest about sampling.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

The SAMPL2 blind prediction challenge: introduction and overview.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Large-scale application of high-throughput molecular mechanics with Poisson-Boltzmann surface area for routine physics-based scoring of protein-ligand complexes

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

Effect of pressure on the phase behavior and structure of water confined between nanoscale hydrophobic and hydrophilic plates.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4832917

5 September 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9795-2

Water inside a hydrophobic cavitand molecule

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25726024

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25726024

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-014-9795-2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25726024%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/GallicchioCCFGH15

1 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:25726024%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

25726024

1 reference