B
Barbora Kozlíková
Researcher at Masaryk University
Publications - 66
Citations - 2010
Barbora Kozlíková is an academic researcher from Masaryk University. The author has contributed to research in topics: Visualization & Biological data visualization. The author has an hindex of 14, co-authored 62 publications receiving 1509 citations. Previous affiliations of Barbora Kozlíková include University of West Bohemia.
Papers
More filters
Journal ArticleDOI
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Eva Chovancová,Antonín Pavelka,Petr Beneš,Ondrej Strnad,Jan Brezovsky,Barbora Kozlíková,Artur Góra,Vilém Šustr,Martin Klvana,Petr Medek,Lada Biedermannová,Jiri Sochor,Jiri Damborsky +12 more
TL;DR: A new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations is presented, and analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating.
Journal ArticleDOI
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Adam Jurcik,David Bednar,Jan Byška,Sérgio M. Marques,Katarína Furmanová,Lukas Daniel,Piia Kokkonen,Jan Brezovsky,Jan Brezovsky,Jan Brezovsky,Ondrej Strnad,Jan Stourac,Antonín Pavelka,Martin Manak,Jiri Damborsky,Barbora Kozlíková +15 more
TL;DR: This work studies the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites to propose novel integrated algorithms that allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations.
Journal ArticleDOI
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
Barbora Kozlíková,Eva Sebestova,Vilém Šustr,Jan Brezovsky,Ondrej Strnad,Lukas Daniel,David Bednar,Antonín Pavelka,Martin Manak,Martin Bezdeka,Petr Benes,Matus Kotry,Artur Góra,Jiri Damborsky,Jiri Sochor +14 more
TL;DR: CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures that provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics.
Journal ArticleDOI
CAVER: algorithms for analyzing dynamics of tunnels in macromolecules
TL;DR: The principles of the CAVER 3.0 algorithms for the identification and analysis of properties of transport pathways both in static and dynamic structures are described and the improved clustering solution for finding tunnels in macromolecules is introduced.
Journal ArticleDOI
Visualization of Biomolecular Structures: State of the Art Revisited
Barbora Kozlíková,Michael Krone,Martin Falk,Norbert Lindow,Marc Baaden,Daniel Baum,Ivan Viola,Ivan Viola,Julius Parulek,Hans-Christian Hege +9 more
TL;DR: The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading, and discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate.