Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses

mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions

(2021) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations

(2021) Shahid Iqbal et al.   BRIEFINGS IN BIOINFORMATICS

Ligand binding free energy and kinetics calculation in 2020

(2020) Vittorio Limongelli   Wiley Interdisciplinary Reviews-Computational Molecular Science

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities

(2020) Ercheng Wang et al.   Journal of Chemical Information and Modeling

Landscape of drug-resistance mutations in kinase regulatory hotspots

(2020) Pora Kim et al.   BRIEFINGS IN BIOINFORMATICS

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

(2020) Bian Li et al.   PLoS Computational Biology

Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein–Protein Interfaces

(2019) Anthony J. Clark et al.   JOURNAL OF MOLECULAR BIOLOGY

Absolute Binding Free Energy Calculation and Design of a Subnanomolar Inhibitor of Phosphodiesterase-10

(2019) Zhe Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

Kinetics of Drug Binding and Residence Time

(2019) Mattia Bernetti et al.   Annual Review of Physical Chemistry

Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations

(2019) Shinnosuke Ikemura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind tests of RNA–protein binding affinity prediction

(2019) Kalli Kappel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug–Target Association Kinetics in Drug Discovery

(2019) Adriaan P. IJzerman et al.   TRENDS IN BIOCHEMICAL SCIENCES

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

(2019) Jianzhong Chen et al.   NUCLEIC ACIDS RESEARCH

QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

(2019) Willem Jespers et al.   Journal of Chemical Theory and Computation

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

(2019) Matteo Aldeghi et al.   ACS Central Science

Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX

(2019) Javier Delgado Blanco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational prediction of protein–protein binding affinities

(2019) Till Siebenmorgen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2018) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

(2018) Fu Chen et al.   RNA

Prediction of enzymatic pathways by integrative pathway mapping

(2018) Sara Calhoun et al.   eLife

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

(2018) Bin Du et al.   TRENDS IN BIOCHEMICAL SCIENCES

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

(2018) Matteo Aldeghi et al.   ACS Central Science

Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations

(2017) Thomas Steinbrecher et al.   JOURNAL OF MOLECULAR BIOLOGY

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

(2016) Inês C. M. Simões et al.   Journal of Chemical Information and Modeling

Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies

(2016) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

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

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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations

(2015) Yan Guan et al.   Molecular BioSystems

Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit

(2015) Simone Fulle et al.   NUCLEIC ACIDS RESEARCH

Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method

(2015) Marharyta Petukh et al.   PLoS Computational Biology

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

(2014) Minghui Li et al.   Journal of Chemical Theory and Computation

Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes

(2014) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

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

Virtual screening using molecular simulations

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

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

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