(Q36029898)

English

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

scientific article published in March 2012

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scholarly article

1 reference

Europe PubMed Central

11 August 2017

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

1 reference

Europe PubMed Central

11 August 2017

Emilio Gallicchio

object named as

Emilio Gallicchio

1

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publication date

1 March 2012

1 reference

Europe PubMed Central

11 August 2017

Computational molecular bioscience

1 reference

Europe PubMed Central

11 August 2017

2

1 reference

Europe PubMed Central

11 August 2017

1

1 reference

Europe PubMed Central

11 August 2017

7-22

1 reference

Europe PubMed Central

11 August 2017

copyright license

Creative Commons Attribution 4.0 International

1 January 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

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Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Alchemical free energy methods for drug discovery: progress and challenges

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Generalized simulated tempering for exploring strong phase transitions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Crystal structures of HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278): implications for drug design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

The AGBNP2 Implicit Solvation Model.

1 reference

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2 October 2017

Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected].

1 reference

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2 October 2017

Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization

1 reference

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2 October 2017

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Computational evaluation of protein-small molecule binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

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=3374582

2 October 2017

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=3374582

2 October 2017

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Ligand configurational entropy and protein binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Calculation of protein-ligand binding affinities.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Crystallography and the design of anti-AIDS drugs: conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

TMC125, a novel next-generation nonnucleoside reverse transcriptase inhibitor active against nonnucleoside reverse transcriptase inhibitor-resistant human immunodeficiency virus type 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

On the theory of noncovalent binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

The many roles of computation in drug discovery

1 reference

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2 October 2017

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=3374582

2 October 2017

Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

2 October 2017

Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the d

1 reference

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11 July 2018

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

1 reference

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11 July 2018

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

1 reference

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23 September 2018

Let's get honest about sampling.

1 reference

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23 September 2018

In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes

1 reference

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23 September 2018

Concentration and pH dependent aggregation of hydrophobic drug molecules and relevance to oral bioavailability.

1 reference

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23 September 2018

Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding

1 reference

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23 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3374582

23 September 2018

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 V

1 reference

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Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein

1 reference

https://pubmed.ncbi.nlm.nih.gov/22708073

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based on heuristic

inferred from PubMed ID database lookup

Linear-scaling soft-core scheme for alchemical free energy calculations

1 reference

https://pubmed.ncbi.nlm.nih.gov/22708073

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enhancing QM/MM molecular dynamics sampling in explicit environments via an orthogonal-space-random-walk-based strategy

1 reference

https://pubmed.ncbi.nlm.nih.gov/22708073

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.4236/CMB.2012.21002

1 reference

Europe PubMed Central

11 August 2017

1 reference

Europe PubMed Central

11 August 2017

1 reference

Europe PubMed Central

11 August 2017

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