GPU‐specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

(2022) Abhishek A. Kognole et al.   Journal of Chemical Theory and Computation

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo

(2022) Yunhui Ge et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Mg2+ Impacts the Twister Ribozyme through Push-Pull Stabilization of Nonsequential Phosphate Pairs

(2020) Abhishek A. Kognole et al.   BIOPHYSICAL JOURNAL

Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)

(2020) Alexander D. MacKerell et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Computational Characterization of Antibody–Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach

(2020) Sunhwan Jo et al.   MOLECULAR PHARMACEUTICS

Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules

(2019) Joel Wahl et al.   Journal of Chemical Information and Modeling

Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation

(2019) Xiaohu Hu et al.   BIOPHYSICAL JOURNAL

Molecular structures of the human Slo1 K+ channel in complex with β4

(2019) Xiao Tao et al.   eLife

Biomolecular Simulations under Realistic Macroscopic Salt Conditions

(2018) Gregory A. Ross et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water

(2018) Delin Sun et al.   Journal of Chemical Theory and Computation

Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations

(2018) Hannah E. Bruce Macdonald et al.   Journal of Chemical Theory and Computation

Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology

(2018) Wenbo Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

(2015) Sirish Kaushik Lakkaraju et al.   Journal of Chemical Information and Modeling

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules

(2015) Wenbo Yu et al.   Journal of Chemical Information and Modeling

Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo

(2015) Gregory A. Ross et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

(2014) Sirish Kaushik Lakkaraju et al.   Journal of Chemical Theory and Computation

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

(2008) Yuqing Deng et al.   JOURNAL OF CHEMICAL PHYSICS