Calculation of protein-ligand binding free energy by using a polarizable potential (Q36609140)

15 August 2017

Calculation of protein-ligand binding free energy by using a polarizable potential (English)

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15 August 2017

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Pengyu Ren

4

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author name string

Dian Jiao

series ordinal

1

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15 August 2017

Pavel A Golubkov

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2

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15 August 2017

Thomas A Darden

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3

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15 August 2017

language of work or name

English

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publication date

21 April 2008

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Proceedings of the National Academy of Sciences of the United States of America

15 August 2017

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15 August 2017

105

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15 August 2017

17

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15 August 2017

6290-6295

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Calculation of protein-ligand binding affinities.

15 August 2017

1 reference

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Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

30 September 2017

1 reference

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1 reference

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Direct calculation of the binding free energies of FKBP ligands

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Calculation of absolute protein-ligand binding free energy from computer simulations

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Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements

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Free energy calculations and ligand binding

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1 reference

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

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30 September 2017

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Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

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Computational approaches to molecular recognition.

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Evaluation of catalytic free energies in genetically modified proteins

28 June 2018

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Electronic effects in the interaction of para-substituted benzamidines with trypsin: the involvement of the pi-electronic density at the central atom of the substituent in binding

28 June 2018

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Molecular dynamics simulations of peptide carboxylate hydration.

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

20 September 2018

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A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors

20 September 2018

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

20 September 2018

1 reference

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Ion solvation thermodynamics from simulation with a polarizable force field

20 September 2018

1 reference

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

20 September 2018

1 reference

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What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?

20 September 2018

1 reference

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Polarizable Force Fields: History, Test Cases, and Prospects

20 September 2018

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Crossref

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Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

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Crossref

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Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

21 January 2018

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12 December 2020

STUDIES ON THE ACTIVE CENTER OF TRYPSIN. THE BINDING OF AMIDINES AND GUANIDINES AS MODELS OF THE SUBSTRATE SIDE CHAIN

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Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

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Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

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Calculation of the Free Energy of Polarization: Quantifying the Effect of Explicitly Treating Electronic Polarization on the Transferability of Force-Field Parameters

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Molecular dynamics simulations of methane hydrate using polarizable force fields

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A new method for predicting binding affinity in computer-aided drug design

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Identifiers

DOI

10.1073/PNAS.0711686105

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15 August 2017

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15 August 2017

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