Rigorous Free Energy Calculations in Structure-Based Drug Design (Q51613137)

8 April 2018

title

Rigorous Free Energy Calculations in Structure-Based Drug Design (English)

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8 April 2018

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Nicolas Foloppe

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8 April 2018

author name string

Julien Michel

series ordinal

1

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8 April 2018

Jonathan W Essex

series ordinal

3

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8 April 2018

publication date

1 September 2010

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8 April 2018

language of work or name

English

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published in

Molecular Informatics

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8 April 2018

volume

29

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issue

8-9

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page(s)

570-578

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

cites work

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Efficient drug lead discovery and optimization

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Development and testing of a general amber force field

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Enhanced Configurational Sampling in Binding Free-Energy Calculations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Towards predictive ligand design with free-energy based computational methods?

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Contributions to the binding free energy of ligands to avidin and streptavidin.

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Hit identification and binding mode predictions by rigorous free energy simulations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Computations of standard binding free energies with molecular dynamics simulations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Grand canonical free-energy calculations of protein-ligand binding.

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Improved protein-ligand docking using GOLD

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Fluorescence polarization competition assay: the range of resolvable inhibitor potency is limited by the affinity of the fluorescent ligand

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

The Development of Replica-Exchange-Based Free-Energy Methods

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Efficient Generalized Born Models for Monte Carlo Simulations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

The parameterization and validation of generalized born models using the pairwise descreening approximation

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Development and optimization of a binding assay for the XIAP BIR3 domain using fluorescence polarization.

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

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Generation and selection of novel estrogen receptor ligands using the de novo structure-based design tool, SkelGen

1 reference

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A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Prediction of the water content in protein binding sites

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Predictions of hydration free energies from all-atom molecular dynamics simulations.

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

A critical assessment of docking programs and scoring functions

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Thermodynamic analysis of mRNA cap binding by the human initiation factor eIF4E via free energy perturbations

1 reference

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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

1 reference

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

1 reference

21 April 2025

https://opencitations.net/index/api/v1/references/10.1002/MINF.201000051

Identifiers

DOI

10.1002/MINF.201000051

1 reference

8 April 2018

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8 April 2018