3 papers
cond-mat.soft2020
Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-range Electrostatics and Mean-field Hydrodynamics
Martin Reinhardt, Neil J. Bruce, Daria B. Kokh +1
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solut…
q-bio.BM2020
A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories
Daria B. Kokha, Bernd Doser, Stefan Richter +3
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are fa…
q-bio.QM2020
Recent progress in molecular simulation methods for drug binding kinetics
Ariane Nunes-Alves, Daria B. Kokh, Rebecca C. Wade
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters.…