4 papers
Three-fold mechanism of inhibition of SARS-CoV-2 infection by the interaction of the spike glycoprotein with heparin
Giulia Paiardi, Stefan Richter, Pasqua Oreste +3
Heparin has been found to have antiviral activity against SARS-CoV-2. Here, by means of sliding window docking, molecular dynamics simulations and biochemical assays, we investigat…
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…
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…
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.…