125 citations · 298 across the 4 of their papers we have counts for
5 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…
Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from tauRAMD simulations
Ariane Nunes-Alves, Daria B. Kokh, Rebecca C. Wade
The protein-ligand residence time, tau, influences molecular function in biological networks and has been recognized as an important determinant of drug efficacy. To predict tau, c…
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.…