(Q35750168)

10 August 2017

title

Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations (English)

1 reference

10 August 2017

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1 reference

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Yue Shi

1

1 reference

10 August 2017

Crystal Z Zhu

series ordinal

2

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10 August 2017

Stephen F Martin

series ordinal

3

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10 August 2017

Pengyu Ren

series ordinal

4

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10 August 2017

language of work or name

English

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publication date

31 January 2012

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Journal of Physical Chemistry B

10 August 2017

published in

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10 August 2017

volume

116

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10 August 2017

issue

5

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10 August 2017

page(s)

1716-1727

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Perspectives on Basis Sets Beautiful: Seasonal Plantings of Diffuse Basis Functions

10 August 2017

cites work

1 reference

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Alchemical free energy methods for drug discovery: progress and challenges

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Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions

12 July 2018

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12 July 2018

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Binding of flexible and constrained ligands to the Grb2 SH2 domain: structural effects of ligand preorganization

12 July 2018

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12 July 2018

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Comparison of entropic contributions to binding in a "hydrophilic" versus "hydrophobic" ligand-protein interaction

12 July 2018

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12 July 2018

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Current status of the AMOEBA polarizable force field

12 July 2018

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12 July 2018

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

12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Calculation of protein-ligand binding affinities.

12 July 2018

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

12 July 2018

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Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

12 July 2018

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The many roles of computation in drug discovery

12 July 2018

1 reference

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Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

12 July 2018

1 reference

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Free energy calculations and ligand binding

12 July 2018

1 reference

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Force fields for protein simulations

12 July 2018

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Trp-cage: Folding free energy landscape in explicit water

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Molecular recognition by SH2 domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

High-affinity mu opioid receptor ligands discovered by the screening of an exhaustively stereodiversified library of 1,5-enediols

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

On the calculation of absolute macromolecular binding free energies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Enthalpy-entropy compensation: a phantom phenomenon

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Unraveling hot spots in binding interfaces: progress and challenges

12 July 2018

1 reference

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Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding

12 July 2018

1 reference

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Entropy-enthalpy compensation: fact or artifact?

12 July 2018

1 reference

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Molecular dynamics simulations of biomolecules: long-range electrostatic effects

12 July 2018

1 reference

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Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes

12 July 2018

1 reference

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Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

12 July 2018

1 reference

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Computational approaches to molecular recognition.

12 July 2018

1 reference

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Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA.

12 July 2018

1 reference

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Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Isergonic relations and their significance for catalysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Enthalpy-entropy compensations in drug-DNA binding studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Heat capacity and entropy changes in processes involving proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Evaluating the Accuracy of the Quasiharmonic Approximation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

A temperature predictor for parallel tempering simulations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Enthalpy-entropy compensation reveals solvent reorganization as a driving force for supramolecular encapsulation in water

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Hydration free energies and entropies for water in protein interiors

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Role of solvent in determining conformational preferences of alanine dipeptide in water.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Ion solvation thermodynamics from simulation with a polarizable force field

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277292

CAVEAT: a program to facilitate the design of organic molecules

25 September 2018

1 reference

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Estimating entropies from molecular dynamics simulations

25 September 2018

1 reference

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Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation

15 November 2018

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12 December 2020

Heat does not come in different colours: entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions

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12 December 2020

Ligand preorganization may be accompanied by entropic penalties in protein-ligand interactions

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12 December 2020

Conformational constraint in protein ligand design and the inconsistency of binding entropy

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12 December 2020

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

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Identifiers

DOI

10.1021/JP210265D

1 reference

10 August 2017

1 reference

10 August 2017

1 reference