(Q30495095)

30 September 2017

Prediction of the water content in protein binding sites (English)

1 reference

30 September 2017

3

William L Jorgensen

1 reference

30 September 2017

2

Julian Tirado-Rives

1 reference

30 September 2017

Julien Michel

1

1 reference

PMCID

2891159

30 September 2017

language of work or name

English

0 references

publication date

1 October 2009

1 reference

Journal of Physical Chemistry B

30 September 2017

1 reference

30 September 2017

113

1 reference

30 September 2017

40

1 reference

30 September 2017

13337-13346

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Exploiting ordered waters in molecular docking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Limitations and lessons in the use of X-ray structural information in drug design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

A dry ligand-binding cavity in a solvated protein.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

From docking false-positive to active anti-HIV agent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Water, water everywhere--except where it matters?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Water at biomolecular binding interfaces

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Strong solute-solute dispersive interactions in a protein-ligand complex

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

The many roles of computation in drug discovery

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Structural insights into the stereochemistry of the cyclooxygenase reaction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Structural basis of the Tanford transition of bovine beta-lactoglobulin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Efficient Generalized Born Models for Monte Carlo Simulations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Efficient drug lead discovery and optimization

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Hit identification and binding mode predictions by rigorous free energy simulations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Classification of water molecules in protein binding sites.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Ligand configurational entropy and protein binding

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Modeling water molecules in protein-ligand docking using GOLD.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Grand canonical Monte Carlo simulations of water in protein environments.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891159

Hydrophilicity of cavities in proteins

26 November 2018

1 reference

12 December 2020

Ligand-protein docking with water molecules

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

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

How many water molecules can be detected by protein crystallography?

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

Identifiers

DOI

10.1021/JP9047456

1 reference

30 September 2017

1 reference

30 September 2017

1 reference

PMCID

2891159