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

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(2016)   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2014) Haiting Lu et al.   BIOORGANIC & MEDICINAL CHEMISTRY

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring

(2014) Sarah Sirin et al.   Journal of Chemical Information and Modeling

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

(2014) Paulius Mikulskis et al.   Journal of Chemical Information and Modeling

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

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

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

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

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

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

(2014) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2014) Paulius Mikulskis et al.   JOURNAL OF MOLECULAR MODELING

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

(2014) Rebecca Sure et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Stephen J. Fox et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space

(2013) Marc Adler et al.   Journal of Chemical Information and Modeling

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

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

FEW: A workflow tool for free energy calculations of ligand binding

(2013) Nadine Homeyer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2013) Frithjof Godschalk et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein

(2012) Jacek Dziedzic et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

(2012) Junmei Wang et al.   Journal of Chemical Information and Modeling

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

(2012) Paulette A. Greenidge et al.   Journal of Chemical Information and Modeling

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

(2012) Samuel Genheden et al.   Journal of Chemical Information and Modeling

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

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

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

(2012) Daniel P. Oehme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2012) Hannes Kopitz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2012) Nadine Homeyer et al.   Molecular Informatics

Will molecular dynamics simulations of proteins ever reach equilibrium?

(2012) Samuel Genheden et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2012) Samuel Genheden et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2012) Anna Kohlmann et al.   ACS Medicinal Chemistry Letters

Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

(2011) Robert Abel et al.   ChemMedChem

Transferability of conformational dependent charges from protein simulations

(2011) Samuel Genheden et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

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

(2011) Samuel Genheden et al.   Journal of Chemical Theory and Computation

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

(2011) Krishna Ravindranathan et al.   Journal of Chemical Theory and Computation

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

(2011) Cristiano R. W. Guimarães   Journal of Chemical Theory and Computation

A challenging system: Free energy prediction for factor Xa

(2011) Hannes G. Wallnoefer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2011) Samuel Genheden   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2011) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2011) Antonella Ciancetta et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2011) Michal Kolář et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

(2011) Samuel Genheden et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities

(2010) Cen Gao et al.   BIOPHYSICAL JOURNAL

Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations

(2010) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes

(2010) Yan Li et al.   Journal of Chemical Information and Modeling

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Ligand Affinities Estimated by Quantum Chemical Calculations

(2010) Pär Söderhjelm et al.   Journal of Chemical Theory and Computation

Nonpolar Solvation Free Energies of Protein−Ligand Complexes

(2010) Samuel Genheden et al.   Journal of Chemical Theory and Computation

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

(2010) Kamila Réblová et al.   Journal of Chemical Theory and Computation

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

(2010) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Explicitly Solvated Ligand Contribution to Continuum Solvation Models for Binding Free Energies: Selectivity of Theophylline Binding to an RNA Aptamer

(2010) Holly Freedman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An MM/3D-RISM Approach for Ligand Binding Affinities

(2010) Samuel Genheden et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach

(2009) Marius Retegan et al.   Journal of Chemical Information and Modeling

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

(2009) Sergio Wong et al.   Journal of Chemical Theory and Computation

Molecular modeling of Protein A affinity chromatography

(2009) Matteo Salvalaglio et al.   JOURNAL OF CHROMATOGRAPHY A

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

(2009) Dian Jiao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2009) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Importance of Ligand Reorganization Free Energy in Protein−Ligand Binding-Affinity Prediction

(2009) Chao-Yie Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

(2008) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Conformational dependence of charges in protein simulations

(2008) Pär Söderhjelm et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2008) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

How Accurate Can a Force Field Become? A Polarizable Multipole Model Combined with Fragment-wise Quantum-Mechanical Calculations

(2008) Pär Söderhjelm et al.   JOURNAL OF PHYSICAL CHEMISTRY A

QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins

(2008) Markus Kaukonen et al.   JOURNAL OF PHYSICAL CHEMISTRY B