Publication details

Real-time visualization of protein empty space with varying parameters

Authors

STRNAD Ondřej ŠUSTR Vilém KOZLÍKOVÁ Barbora SOCHOR Jiří

Type Article in Proceedings
Conference Proceedings of Biotechno
MU Faculty or unit

Faculty of Informatics

Citation
Field Informatics
Keywords protein; empty space; void; visualization; real-time; cavity
Description Exploration of empty space inside protein structures is playing a crucial role in protein engineering and drug design. Such empty space inside protein can be utilized for design of protein mutations. The importance of empty space is also based on its ability to accept a small ligand molecule which can react with the protein. The product of such reaction can form a basis of new medications. Many algorithms enabling computation of these empty spaces, often marked as voids, have been published and their results were evaluated by protein engineers to confirm their chemical relevance. However, not each void of the protein can be considered as a target point of ligand binding. Thus the following examination and assessment of all voids has to be performed. In this phase the visual representation of voids is very valuable and substantially decreases time of this evaluation phase. In this paper, we introduce a novel algorithm for visualization and further evaluation of voids in real-time. This user driven approach enables to compute and display empty space that satisfies the input parameters instantly. Basically, these parameters include setting of minimal desired width of the voids. The values of these parameters can be changed by the user anytime and the changes are immediately displayed and prepared for further exploration.
Related projects: