Blar i Department of Informatics på forfatter "Byska, Jan"

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    • Comparative Visualization of Protein Secondary Structures 

      Kocincova, Lucia; Jaresova, Miroslava; Byska, Jan; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein ...

    • Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases 

      Abboud, Angèle; Bedoucha, Pierre; Byska, Jan; Arnesen, Thomas; Reuter, Nathalie (Journal article; Peer reviewed, 2020)
      N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal ...

    • Interactive Exploration of Ligand Transportation through Protein Tunnels 

      Furmanova, Katarina; Jaresova, Miroslava; Byska, Jan; Jurcik, Adam; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex ...

    • Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes 

      Furmanová, Katarína; Jurčík, Adam; Kozlíková, Barbora; Hauser, Helwig; Byska, Jan (Journal article; Peer reviewed, 2020)
      When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more ...

    • 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. ...

    • Visual exploration of large normal mode spaces to study protein flexibility 

      Bedoucha, Pierre; Reuter, Nathalie; Hauser, Helwig; Byska, Jan (Journal article; Peer reviewed, 2020-05-22)
      When studying the function of proteins, biochemists utilize normal mode decomposition to enable the analysis of structural changes on time scales that are too long for molecular dynamics simulation. Such a decomposition ...