The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (Q27012984)

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4 March 2020

review article

2 references

22 August 2022

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (English)

1 reference

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pharmaceutical preparation

4 March 2020

main subject

drug discovery

0 references

1 reference

biomedical investigative technique

6 August 2019

1 reference

19 September 2019

1 reference

1

1 reference

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4 March 2020

Ulf Ryde

series ordinal

2

1 reference

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4 March 2020

author name string

Ulf Ryde

series ordinal

2

1 reference

language of work or name

1 reference

2 April 2015

1 reference

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Expert Opinion on Drug Discovery

4 March 2020

1 May 2015

1 reference

22 August 2022

5 references

6 August 2019

19 September 2019

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4 March 2020

22 August 2022

10

2 references

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4 March 2020

issue

5

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4 March 2020

page(s)

449-461

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Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported

4 March 2020

copyright license

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6 August 2019

19 September 2019

Creative Commons Attribution-NonCommercial-NoDerivatives

22 August 2022

1 reference

13 September 2020

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

1 reference

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Develop and test a solvent accessible surface area-based model in conformational entropy calculations

21 March 2017

1 reference

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

21 March 2017

1 reference

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

21 March 2017

1 reference

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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

7 April 2017

1 reference

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Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

28 September 2017

1 reference

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Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

28 September 2017

1 reference

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A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.

28 September 2017

1 reference

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Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.

28 September 2017

1 reference

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Application of MM-GB/SA and WaterMap to SRC Kinase Inhibitor Potency Prediction

28 September 2017

1 reference

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Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

28 September 2017

1 reference

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Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.

28 September 2017

1 reference

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Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.

28 September 2017

1 reference

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MM/GBSA binding energy prediction on the PDBbind data set: successes, failures, and directions for further improvement.

28 September 2017

1 reference

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Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model

28 September 2017

1 reference

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Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

28 September 2017

1 reference

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Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

28 September 2017

1 reference

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Virtual screening using molecular simulations

28 September 2017

1 reference

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

28 September 2017

1 reference

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Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities

28 September 2017

1 reference

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Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

28 September 2017

1 reference

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Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer

28 September 2017

1 reference

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Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.

28 September 2017

1 reference

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MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

28 September 2017

1 reference

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Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

28 September 2017

1 reference

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MM-GB/SA rescoring of docking poses in structure-based lead optimization.

28 September 2017

1 reference

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Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

28 September 2017

1 reference

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

28 September 2017

1 reference

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What are the dielectric "constants" of proteins and how to validate electrostatic models?

28 September 2017

1 reference

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Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

28 September 2017

1 reference

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Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site

28 September 2017

1 reference

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g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

31 May 2018

1 reference

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Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model

31 May 2018

1 reference

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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

31 May 2018

1 reference

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A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

31 May 2018

1 reference

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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

31 May 2018

1 reference

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

31 May 2018

1 reference

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An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods

21 January 2018

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Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.

21 January 2018

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Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

21 January 2018

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Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

21 January 2018

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Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.

21 January 2018

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Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

21 January 2018

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Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations

21 January 2018

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Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models

21 January 2018

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FEW: a workflow tool for free energy calculations of ligand binding.

21 January 2018

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Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases

21 January 2018

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Improved ligand binding energies derived from molecular dynamics: replicate sampling enhances the search of conformational space

21 January 2018

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Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease.

21 January 2018

1 reference

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An MM/3D-RISM approach for ligand binding affinities.

21 January 2018

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How accurate are continuum solvation models for drug-like molecules?

21 January 2018

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Implicit nonpolar solvent models

21 January 2018

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Ligand Affinities Estimated by Quantum Chemical Calculations

21 January 2018

1 reference

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Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations

21 January 2018

1 reference

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Conformational dependence of charges in protein simulations.

21 January 2018

1 reference

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An improved method to predict the entropy term with the MM/PBSA approach.

21 January 2018

1 reference

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Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes

21 January 2018

1 reference

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Evaluating the Accuracy of the Quasiharmonic Approximation

21 January 2018

1 reference

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Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin

21 January 2018

1 reference

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Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

21 January 2018

1 reference

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QM/MM-PBSA method to estimate free energies for reactions in proteins.

21 January 2018

1 reference

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Exploring the binding of inhibitors derived from tetrabromobenzimidazole to the CK2 protein using a QM/MM-PB/SA approach.

21 January 2018

1 reference

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Molecular modeling of protein A affinity chromatography.

21 January 2018

1 reference

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Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

21 January 2018

1 reference

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Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

21 January 2018

1 reference

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Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody

21 January 2018

1 reference

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Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

21 January 2018

1 reference

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Molecular recognition by beta-cyclodextrin derivatives: FEP vs MM/PBSA study

21 January 2018

1 reference

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Unravelling Hot Spots: a comprehensive computational mutagenesis study

21 January 2018

1 reference

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Assessment of Solvation Effects on Calculated Binding Affinity Differences: Trypsin Inhibition by Flavonoids as a Model System for Congeneric Series

21 January 2018

1 reference

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Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

21 January 2018

1 reference

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The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

21 January 2018

1 reference

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Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation

21 January 2018

1 reference

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How to obtain statistically converged MM/GBSA results.

21 January 2018

1 reference

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Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.

28 November 2018

1 reference

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

28 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Validation and use of the MM-PBSA approach for drug discovery

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

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

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Test MM-PB/SA on true conformational ensembles of protein-ligand complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A challenging system: free energy prediction for factor Xa

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A QM/MM study of the binding of RAPTA ligands to cathepsin B

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections

1 reference

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12 December 2020

Will molecular dynamics simulations of proteins ever reach equilibrium?

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Blind Prediction of Binding Affinities for Charged Supramolecular Host–Guest Systems: Achievements and Shortcomings of DFT-D3

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A computational approach to enzyme design: predicting ω-aminotransferase catalytic activity using docking and MM-GBSA scoring

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

A Direct Comparison of the MM-GB/SA Scoring Procedure and Free-Energy Perturbation Calculations Using Carbonic Anhydrase as a Test Case: Strengths and Pitfalls of Each Approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Nonpolar Solvation Free Energies of Protein-Ligand Complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

Ligand binding affinity prediction by linear interaction energy methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/25835573

12 December 2020

10.1517/17460441.2015.1032936

Identifiers

DOI

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25835573%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25835573%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

PubMed publication ID

25835573

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25835573%20AND%20SRC:MED&resulttype=core&format=json