Blar i Bergen Open Research Archive på forfatter "Ulbrich, Pavol"
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sMolBoxes: Dataflow Model for Molecular Dynamics Exploration
Ulbrich, Pavol; Waldner, Manuela; Furmanová, Katarína; Marques, Sergio M.; Bednář, David; Kozlíková, Barbora; Byska, Jan (Journal article; Peer reviewed, 2023)We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible ... -
Visual Analysis of Ligand Trajectories in Molecular Dynamics
Jurcik, Adam; Furmanova, Katarina; Byska, Jan; Vonasek, Vojtech; Vavra, Ondrej; Ulbrich, Pavol; Hauser, Helwig; Kozlikova, Barbora (Journal article; Peer reviewed, 2019)In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. ...