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

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

(2012) Nadine Homeyer et al.   Molecular Informatics

Advances and applications of binding affinity prediction methods in drug discovery

(2011) Marco Daniele Parenti et al.   BIOTECHNOLOGY ADVANCES

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes

(2010) Pedro A. Valiente et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computer-aided drug design platform using PyMOL

(2010) Markus A. Lill et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening

(2009) Giulio Rastelli et al.   Chemical Biology & Drug Design

Linear Interaction Energy (LIE) Method in Lead Discovery and Optimization

(2008) Hermes Luis de Amorim et al.   CURRENT DRUG TARGETS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases

(2008) Ileana Stoica et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

7-Fluoroindazoles as Potent and Selective Inhibitors of Factor Xa†

(2007) Yu-Kai Lee et al.   JOURNAL OF MEDICINAL CHEMISTRY