Visualizations in CAVER Analyst

Software tool for analysis and visualization of protein structures

We present the latest results coming from the collaboration between the visualization group at the Faculty of Informatics at the Masaryk University in Brno and the Institute of Computer Graphics and Algorithms at TU Wien. We focused namely on conveying the information about tunnels in proteins detected by the CAVER algorithm in molecular dynamics simulations. All presented techniques are integrated in the CAVER Analyst software tool and will be a part of its next release. However, the alpha version is available upon request.

Publications related to CAVER and CAVER Analyst tools are available here:
CAVER 3.0 was published in PLoS Computational Biology, CAVER Analyst was published in Bioinformatics.

Visual exploration of tunnel bottleneck over time

In this paper, we help the biochemist to select the most interesting tunnels (i.e., stable over time) and for each of them, explore their bottleneck in detail. This is reached by using visual abstraction of the bottleneck crosscut and encoding the information about its surrounding amino acids and its shape and their changes over time.

The publication can be found here.
Short video explaining the technique:


Visual exploration of tunnel along its centerline over time

In this paper, our aim was to extend the previous idea to the exploration of whole tunnel along its centerline over time. We present the evolution of the tunnel width which helps to detect interesting sites along its centerline. Additionally, we encode the information about the amino acids in the close vicinity of the tunnel and the amount of influence they have on the tunnel. This helps to reveal the critical parts of the tunnel (e.g., bottlenecks, highly unstable parts) and the amino acids causing this feature or behavior.

The publication can be found here.
Short video explaining the technique:

Visual analysis of water trajectories over time

In our latest, yet unpublished research, we focus on the visual exploration of trajectories of water molecules flowing through a protein over time. Simulations of molecular dynamics can contain thousands of water molecules and their trajectories are too complex to be understood from traditional 3D visualization. Therefore, we propose a set of methods for categorization, clustering, and visualization of these trajectories which help to reveal the most interesting and important water molecules in a fast and intuitive way.

The preliminary version of our publication can be found here. Please, treat it confidentially.
Short video explaining the technique:

Visual exploration of protein-protein interactions

Recently, our area of interest expanded to the field of visual exploration of protein-protein interactions. Here we propose a system for the exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones. The set of proposed visual techniques serves for quided exploration of the configuration space which helps the domain experts to select the most proteomically relevant contact zones and explore them on different levels of detail. The system integrates a set of methods following the workflow of proteomics experts.

The preliminary version of our publication can be found here. Please, treat it confidentially.
Short video explaining the technique:



For further details or questions, please contact the leading persons of this project, Barbora Kozlikova from the Masaryk University and Ivan Viola from TU Wien.



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