Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors (Q34530495)

2 August 2017

title

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors (English)

1 reference

2 August 2017

James Luccarelli

1

0 references

William L. Jorgensen

series ordinal

4

object named as

William L Jorgensen

1 reference

2 August 2017

3

Julian Tirado-Rives

1 reference

2 August 2017

Julien Michel

2

1 reference

2 August 2017

publication date

1 January 2010

1 reference

Journal of Chemical Theory and Computation

2 August 2017

published in

1 reference

2 August 2017

volume

6

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2 August 2017

issue

12

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2 August 2017

page(s)

3850-3856

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Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

2 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Prediction of the water content in protein binding sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Healthy skepticism: assessing realistic model performance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Efficient drug lead discovery and optimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Very fast prediction and rationalization of pKa values for protein-ligand complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

From docking false-positive to active anti-HIV agent

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Structural basis for p38alpha MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

VMD: visual molecular dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3029023

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21278915

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Rigorous Free Energy Calculations in Structure-Based Drug Design

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21278915

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT100504H

1 reference

2 August 2017

1 reference

2 August 2017

1 reference