Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

(2016) Majda Misini Ignjatović et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Concepts and protocols for electrostatic free energies

(2016) Thomas Simonson et al.   MOLECULAR SIMULATION

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder 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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

(2014) Paulius Mikulskis et al.   Journal of Chemical Information and Modeling

Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent

(2014) Toru Ekimoto et al.   Journal of Chemical Theory and Computation

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

(2014) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

FXR is a molecular target for the effects of vertical sleeve gastrectomy

(2014) Karen K. Ryan et al.   NATURE

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

(2013) Clara D. Christ et al.   Journal of Chemical Information and Modeling

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

(2013) Joseph W. Kaus et al.   Journal of Chemical Theory and Computation

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation

(2013) Maria M. Reif et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Improving the Efficiency of Protein–Ligand Binding Free-Energy Calculations by System Truncation

(2012) Samuel Genheden et al.   Journal of Chemical Theory and Computation

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties

(2011) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

(2011) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

(2010) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Healthy skepticism: assessing realistic model performance

(2009) Scott P. Brown et al.   DRUG DISCOVERY TODAY

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

(2007) Haizhen Zhong et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Evaluating Rotational Diffusion from Protein MD Simulations†

(2007) Vance Wong et al.   JOURNAL OF PHYSICAL CHEMISTRY B