Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics

(2017) Joseph A. Morrone et al.   Journal of Chemical Theory and Computation

Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX

(2017) Joseph A. Morrone et al.   Journal of Chemical Theory and Computation

Protein–ligand docking using FFT based sampling: D3R case study

(2017) Dzmitry Padhorny et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

(2016) Sergei Grudinin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

(2015) Chengfei Yan et al.   Journal of Chemical Information and Modeling

Energy Minimization on Manifolds for Docking Flexible Molecules

(2015) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li 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

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening

(2014) Ambrish Roy et al.   BIOINFORMATICS

Encounter complexes and dimensionality reduction in protein–protein association

(2014) Dima Kozakov et al.   eLife

Rigid Body Energy Minimization on Manifolds for Molecular Docking

(2012) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B