(Q37439036)

20 August 2017

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

1 reference

20 August 2017

3

William L Jorgensen

1 reference

20 August 2017

2

Julian Tirado-Rives

1 reference

20 August 2017

Julien Michel

1

1 reference

PMC publication ID

2783447

20 August 2017

language of work or name

English

0 references

publication date

1 October 2009

1 reference

Journal of the American Chemical Society

20 August 2017

1 reference

20 August 2017

131

1 reference

20 August 2017

42

1 reference

20 August 2017

15403-15411

1 reference

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Efficient drug lead discovery and optimization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

MM-GB/SA rescoring of docking poses in structure-based lead optimization.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

From docking false-positive to active anti-HIV agent

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Water at biomolecular binding interfaces

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

The many roles of computation in drug discovery

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

VMD: visual molecular dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Determination of the interfacial water content in protein-protein complexes from free energy simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Free energies and entropies of water molecules at the inhibitor-protein interface of DNA gyrase

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Hit identification and binding mode predictions by rigorous free energy simulations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

A molecular dynamics approach to study the importance of solvent in protein interactions

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

On the contribution of water-mediated interactions to protein-complex stability

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Classification of water molecules in protein binding sites.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Thermodynamics of buried water clusters at a protein-ligand binding interface

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

5-Cyanopyrimidine derivatives as a novel class of potent, selective, and orally active inhibitors of p38alpha MAP kinase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2783447

4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor kinase and their bioisosteric relationship to the 4-anilino-6,7-dialkoxyquinazoline inhibitors

2 September 2018

1 reference

12 December 2020

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

1 reference

12 December 2020

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

The effect of water displacement on binding thermodynamics: concanavalin A

1 reference

12 December 2020

Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

1 reference

12 December 2020

Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes.

1 reference

12 December 2020

Efficient Generalized Born Models for Monte Carlo Simulations.

1 reference

12 December 2020

Automatic Control of Solvent Density in Grand Canonical Ensemble Monte Carlo Simulations.

1 reference

12 December 2020

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

1 reference

12 December 2020

Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes.

1 reference

12 December 2020

Tyrosine kinase inhibitors. 5. Synthesis and structure-activity relationships for 4-[(phenylmethyl)amino]- and 4-(phenylamino)quinazolines as potent adenosine 5'-triphosphate binding site inhibitors of the tyrosine kinase domain of the epidermal gro

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA906058W

1 reference

20 August 2017

1 reference

PMC publication ID

2783447

20 August 2017

PubMed publication ID

19778066

1 reference

PMC publication ID

2783447