23 citations · 79 across the 10 of their papers we have counts for
4 papers · 1 filter
Derivation of the Sample-Size Scaling of TWO-NN Intrinsic-Dimension Estimates from Molecular Dynamics Trajectories
Riccardo Capelli
The intrinsic dimension of a dataset is the number of independent directions needed to describe the space occupied by its data. Nearest-neighbor estimators infer it from how the pr…
Kinetic rates calculation via non-equilibrium dynamics
Bruno Stegani, Riccardo Capelli
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand com…
Ephemeral ice-like local environments in classical rigid models of liquid water
Riccardo Capelli, Francesco Muniz-Miranda, Giovanni M. Pavan
Despite great efforts over the past 50 years, the simulation of water still presents significant challenges and open questions. At room temperature and pressure, the collective mol…
Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics
Riccardo Capelli, Paolo Carloni, Michele Parrinello
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics…