• 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. ...