(Q36609140)

15 August 2017

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

1 reference

15 August 2017

1 reference

Pengyu Ren

4

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author name string

Dian Jiao

series ordinal

1

1 reference

15 August 2017

Pavel A Golubkov

series ordinal

2

1 reference

15 August 2017

Thomas A Darden

series ordinal

3

1 reference

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Modeling electrostatic effects in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

The Amber biomolecular simulation programs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Direct calculation of the binding free energies of FKBP ligands

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Calculation of absolute protein-ligand binding free energy from computer 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=2359813

Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular 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=2359813

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

The many roles of computation in drug discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Free energy calculations and ligand binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Force fields for protein 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=2359813

A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Computational approaches to molecular recognition.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Evaluation of catalytic free energies in genetically modified proteins

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Molecular dynamics simulations of peptide carboxylate hydration.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Ion solvation thermodynamics from simulation with a polarizable force field

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2359813

Polarizable Force Fields: History, Test Cases, and Prospects

20 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0711686105

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0711686105

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

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Molecular dynamics simulations of methane hydrate using polarizable force fields

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0711686105

1 reference

15 August 2017

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15 August 2017

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