(Q30422862)

14 August 2017

Perspective: Alchemical free energy calculations for drug discovery (English)

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14 August 2017

1 reference

David L Mobley

1

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author name string

Pavel V Klimovich

series ordinal

2

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PMCID

3537745

14 August 2017

language of work or name

English

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publication date

1 December 2012

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Journal of Chemical Physics

14 August 2017

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14 August 2017

137

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14 August 2017

23

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14 August 2017

230901

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Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Separated topologies--a method for relative binding free energy calculations using orientational restraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Alchemical prediction of hydration free energies for SAMPL.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Recent theoretical and computational advances for modeling protein-ligand binding affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Using free energy of binding calculations to improve the accuracy of virtual screening predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Free energy calculations of protein-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Alchemical free energy methods for drug discovery: progress and challenges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Advances in all atom sampling methods for modeling protein-ligand binding affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Improved ligand-protein binding affinity predictions using multiple binding modes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Towards accurate free energy calculations in ligand protein-binding studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Basic ingredients of free energy calculations: a review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Prediction of the water content in protein binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Strategies and tactics for optimizing the Hit-to-Lead process and beyond--a computational chemistry perspective.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Statistical analysis of the effects of common chemical substituents on ligand potency

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Virtual screening strategies in drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Predicting absolute ligand binding free energies to a simple model site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

A critical assessment of docking programs and scoring functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Virtual ligand screening: strategies, perspectives and limitations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Computational chemistry-driven decision making in lead generation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Virtual screening of chemical libraries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

The many roles of computation in drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Lead discovery using molecular docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Structure-based design of inhibitors specific for bacterial thymidylate synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Theoretical calculation of relative binding affinity in host-guest systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Structural analysis of a series of antiviral agents complexed with human rhinovirus 14.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Computer-aided molecular design under the SWOTlight.

20 June 2018

1 reference

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

21 January 2018

1 reference

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

21 January 2018

1 reference

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

21 January 2018

1 reference

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

1 reference

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

1 reference

Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations

21 January 2018

1 reference

Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.

21 January 2018

1 reference

Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach

21 January 2018

1 reference

Structure-guided design of AMP mimics that inhibit fructose-1,6-bisphosphatase with high affinity and specificity

21 January 2018

1 reference

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

21 January 2018

1 reference

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.

21 January 2018

1 reference

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

21 January 2018

1 reference

Calculation of the Redox Potential of the Protein Azurin and Some Mutants

21 January 2018

1 reference

Molecular Modeling-Guided Site-Directed Mutagenesis of Cytochrome P450 2D6

21 January 2018

1 reference

Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin

21 January 2018

1 reference

Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors.

21 January 2018

1 reference

Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series

21 January 2018

1 reference

Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects

21 January 2018

1 reference

Hit identification and binding mode predictions by rigorous free energy simulations

21 January 2018

1 reference

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

21 January 2018

1 reference

Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.

21 January 2018

1 reference

Let's get honest about sampling.

21 January 2018

1 reference

Alchemical free energy calculations and multiple conformational substates

21 January 2018

1 reference

Hamiltonian replica exchange molecular dynamics using soft-core interactions

21 January 2018

1 reference

Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

21 January 2018

1 reference

Computing conformational free energy by deactivated morphing

21 January 2018

1 reference

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering.

21 January 2018

1 reference

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

21 January 2018

1 reference

Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3537745

Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin

26 November 2018

1 reference

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

21 January 2018

1 reference

12 December 2020

Excess free energy of liquids from molecular dynamics simulations. Application to water models

1 reference

12 December 2020

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

1 reference

12 December 2020

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

1 reference

12 December 2020

Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein

1 reference

12 December 2020

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

1 reference

12 December 2020

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020

Can we use docking and scoring for hit-to-lead optimization?

1 reference

12 December 2020

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

1 reference

12 December 2020

Free energy calculations by computer simulation

1 reference

12 December 2020

A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase

1 reference

12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.4769292

1 reference

14 August 2017

1 reference

14 August 2017

1 reference

PMCID

3537745