gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies

(2021) Vilhelm Ekberg et al.   Journal of Chemical Theory and Computation

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

A Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies

(2019) D'Artagnan Greene et al.   Journal of Chemical Information and Modeling

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

SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

(2018) Justina Jankauskaitė et al.   BIOINFORMATICS

Assessing the Performance of MM/PBSA, MM/GBSA, and QM–MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

(2018) Sushil K. Mishra et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction Entropy for Computational Alanine Scanning

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

Interaction entropy for protein-protein binding

(2017) Zhaoxi Sun et al.   JOURNAL OF CHEMICAL PHYSICS

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

(2017) Li Xiao et al.   Journal of Chemical Theory and Computation

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning

(2015) C. Paissoni et al.   COMPUTER PHYSICS COMMUNICATIONS

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

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

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

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

A consistent force field parameter set for zwitterionic amino acid residues

(2014) Anselm H. C. Horn   JOURNAL OF MOLECULAR MODELING

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

Numerical Poisson–Boltzmann model for continuum membrane systems

(2012) Wesley M. Botello-Smith et al.   CHEMICAL PHYSICS LETTERS

Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations

(2012) Jun Wang et al.   Journal of Chemical Theory and Computation

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

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

Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

(2012) Michaela Wimmerová et al.   PLoS One

Parallel distributed computing using Python

(2011) Lisandro D. Dalcin et al.   ADVANCES IN WATER RESOURCES

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

Assessment of linear finite-difference Poisson–Boltzmann solvers

(2010) Jun Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane

(2010) Keith M. Callenberg et al.   PLoS One

Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers

(2009) Qin Cai et al.   Journal of Chemical Theory and Computation

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

(2009) Giulio Rastelli et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY