Barbora Kozlikova - Academia.edu (original) (raw)
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Papers by Barbora Kozlikova
2015 7th International Conference on Games and Virtual Worlds for Serious Applications (VS-Games), 2015
Computer Graphics Forum, 2015
: Proposed methods for a set of tunnels in protein structures computed within an ensemble of mole... more : Proposed methods for a set of tunnels in protein structures computed within an ensemble of molecular dynamics. (a) One timestep of DhaA haloalkane dehalogenase with 39 tunnels leading to one active site; (b) heat map of one selected tunnel (STH) showing the evolution of the tunnel width over time (the left side represents the active site, the right side represents the tunnel gorge, and the vertical axis represents the time); (c) detailed exploration of the tunnel bottleneck contour (collar) over time; (d) 3D tunnel cut right at the bottleneck shown together with the surrounding amino acids.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015
IEEE Transactions on Visualization and Computer Graphics, 2015
In this paper we propose a novel method for the interactive exploration of protein tunnels. The b... more In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.
Structural properties of molecules are of primary concern in many fields. This report provides a ... more Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
Proceedings of the 5th international conference on Computer graphics, virtual reality, visualisation and interaction in Africa - AFRIGRAPH '07, 2007
This paper presents two novel techniques for visualization of tunnels in complex molecules of pro... more This paper presents two novel techniques for visualization of tunnels in complex molecules of proteins. Long-term research in the field of protein analysis proved that the reactivity of the protein molecule depends on the presence of tunnels. These structures are very important mainly in the process of finding new pharmaceuticals. Visualization of a tunnel is the next very important step after the analysis because it enables the biochemists to determine the crucial regions of the tunnel, which can have a substantial effect in the process of designing new medication.
2015 7th International Conference on Games and Virtual Worlds for Serious Applications (VS-Games), 2015
Computer Graphics Forum, 2015
: Proposed methods for a set of tunnels in protein structures computed within an ensemble of mole... more : Proposed methods for a set of tunnels in protein structures computed within an ensemble of molecular dynamics. (a) One timestep of DhaA haloalkane dehalogenase with 39 tunnels leading to one active site; (b) heat map of one selected tunnel (STH) showing the evolution of the tunnel width over time (the left side represents the active site, the right side represents the tunnel gorge, and the vertical axis represents the time); (c) detailed exploration of the tunnel bottleneck contour (collar) over time; (d) 3D tunnel cut right at the bottleneck shown together with the surrounding amino acids.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015
IEEE Transactions on Visualization and Computer Graphics, 2015
In this paper we propose a novel method for the interactive exploration of protein tunnels. The b... more In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.
Structural properties of molecules are of primary concern in many fields. This report provides a ... more Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
Proceedings of the 5th international conference on Computer graphics, virtual reality, visualisation and interaction in Africa - AFRIGRAPH '07, 2007
This paper presents two novel techniques for visualization of tunnels in complex molecules of pro... more This paper presents two novel techniques for visualization of tunnels in complex molecules of proteins. Long-term research in the field of protein analysis proved that the reactivity of the protein molecule depends on the presence of tunnels. These structures are very important mainly in the process of finding new pharmaceuticals. Visualization of a tunnel is the next very important step after the analysis because it enables the biochemists to determine the crucial regions of the tunnel, which can have a substantial effect in the process of designing new medication.