Home // BIOTECHNO 2013, The Fifth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies // View article

Real-time Visualization of Protein Empty Space with Varying Parameters

Authors:
Ondrej Strnad
Vilem Sustr
Barbora Kozlikova
Jiri Sochor

Keywords: protein, empty space, void, visualization, real-time, cavity

Abstract:
Exploration of the empty space inside protein structures is playing a crucial role in protein engineering and drug design. This empty space inside proteins can be utilized for the design of protein mutations. The importance of this empty space is also based on its ability to accept a small ligand molecule which can react with the protein. The product of such a reaction can form the 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 all voids of a protein can be considered as a target point of ligand binding. Thus, the following examination and assessment of all voids must 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 the visualization and further evaluation of these 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.

Pages: 65 to 70

Copyright: Copyright (c) IARIA, 2013

Publication date: March 24, 2013

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-260-8

Location: Lisbon, Portugal

Dates: from March 24, 2013 to March 29, 2013