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

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

Molecular Dynamics of Methyl Viologen-Cucurbit[n]uril Complexes in Aqueous Solution

(2010) Musa I. El-Barghouthi 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

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined

(2010) Joseph M. Hayes et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design

(2009) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational dependence of charges in protein simulations

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

Molecular dynamics simulations and MM–PBSA calculations of the cyclodextrin inclusion complexes with 1-alkanols, para-substituted phenols and substituted imidazoles

(2007) M.I. El-Barghouthi et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM