Correcting electrostatic artifacts due to net‐charge changes in the calculation of ligand binding free energies

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

(2018) Haohao Fu et al.   Journal of Chemical Information and Modeling

Saturation Mutagenesis by Efficient Free-Energy Calculation

(2018) Zuzana Jandova et al.   Journal of Chemical Theory and Computation

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding

(2018) Israel Cabeza de Vaca et al.   Journal of Chemical Theory and Computation

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

(2018) Wei Chen et al.   Journal of Chemical Theory and Computation

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method

(2018) Toru Ekimoto et al.   Journal of Chemical Theory and Computation

Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties

(2017) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

(2017) Jan Walther Perthold et al.   Journal of Chemical Theory and Computation

Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C

(2016) Xiaojie Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points

(2016) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization

(2015) Maria M. Reif et al.   THEORETICAL CHEMISTRY ACCOUNTS

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

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

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

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

(2012) Jason A. Wallace et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors

(2012) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Protein–Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations

(2012) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

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

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

(2011) Hironori Kokubo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities

(2011) Jožica Dolenc et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Single Mutation Induced H3N2 Hemagglutinin Antibody Neutralization: A Free Energy Perturbation Study

(2008) Ruhong Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B