Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

(2017) Matteo Aldeghi et al.   Journal of Chemical Information and Modeling

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations

(2017) Ido Y. Ben-Shalom et al.   Journal of Chemical Information and Modeling

Interaction Entropy for Computational Alanine Scanning

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

Characterizing Drug–Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches

(2017) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study

(2017) Henrik Keränen et al.   Journal of Chemical Theory and Computation

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

(2017) Bernd Kuhn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

(2016) Huiyong Sun et al.   Journal of Chemical Theory and Computation

Calculation of Configurational Entropy Differences from Conformational Ensembles Using Gaussian Mixtures

(2016) Gergely Gyimesi et al.   Journal of Chemical Theory and Computation

Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates

(2016) Simon Hikiri et al.   Journal of Chemical Theory and Computation

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

(2016) Shan Chang et al.   RNA Biology

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery

(2016) Huiyong Sun et al.   Scientific Reports

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

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method

(2015) Hwanho Choi et al.   Journal of Chemical Theory and Computation

Enthalpy–Entropy Compensation upon Molecular Conformational Changes

(2015) Mazen Ahmad et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

The drug–target residence time model: a 10-year retrospective

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

(2015) Huiyong Sun et al.   Scientific Reports

Finding chemical drugs for genetic diseases

(2014) Hui-Yong Sun et al.   DRUG DISCOVERY TODAY

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

Discovery of Novel Inhibitors Targeting the Macrophage Migration Inhibitory Factor via Structure-Based Virtual Screening and Bioassays

(2014) Lei Xu et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy

(2013) Hui-Yong Sun et al.   Journal of Chemical Information and Modeling

Molecular Dynamic Investigations of the Mutational Effects on Structural Characteristics and Tunnel Geometry in CYP17A1

(2013) Ying-Lu Cui et al.   Journal of Chemical Information and Modeling

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches

(2013) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

(2013) Samuel Genheden et al.   Journal of Chemical Theory and Computation

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

Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding

(2013) Li Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extreme Entropy–Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease

(2012) Nancy M. King et al.   ACS Chemical Biology

A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

(2012) Hui-Yong Sun et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Conformational Adaptation Drives Potent, Selective and Durable Inhibition of the Human Protein Methyltransferase DOT1L

(2012) Aravind Basavapathruni et al.   Chemical Biology & Drug Design

Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study

(2012) Attilio V. Vargiu et al.   INORGANIC CHEMISTRY

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

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis

(2012) Weiwei Xue et al.   Journal of Chemical Information and Modeling

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Calculation of Molecular Entropies Using Temperature Integration

(2012) Kim Sharp   Journal of Chemical Theory and Computation

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

(2012) Tingjun Hou et al.   JOURNAL OF PROTEOME RESEARCH

Will molecular dynamics simulations of proteins ever reach equilibrium?

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

Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435

(2011) Weiwei Xue et al.   ANTIVIRAL RESEARCH

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

Drug–target residence time: critical information for lead optimization

(2010) Hao Lu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function

(2008) Peter J. Tummino et al.   BIOCHEMISTRY

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

(2008) William L. Jorgensen et al.   Journal of Chemical Theory and Computation