NexTech 2021 Congress
October 03, 2021 to October 07, 2021 - Barcelona, Spain

  • UBICOMM 2021, The Fifteenth International Conference on Mobile Ubiquitous Computing, Systems, Services and Technologies
  • ADVCOMP 2021, The Fifteenth International Conference on Advanced Engineering Computing and Applications in Sciences
  • SEMAPRO 2021, The Fifteenth International Conference on Advances in Semantic Processing
  • AMBIENT 2021, The Eleventh International Conference on Ambient Computing, Applications, Services and Technologies
  • EMERGING 2021, The Thirteenth International Conference on Emerging Networks and Systems Intelligence
  • DATA ANALYTICS 2021, The Tenth International Conference on Data Analytics
  • GLOBAL HEALTH 2021, The Tenth International Conference on Global Health Challenges
  • CYBER 2021, The Sixth International Conference on Cyber-Technologies and Cyber-Systems

SoftNet 2021 Congress
October 03, 2021 to October 07, 2021 - Barcelona, Spain

  • ICSEA 2021, The Sixteenth International Conference on Software Engineering Advances
  • ICSNC 2021, The Sixteenth International Conference on Systems and Networks Communications
  • CENTRIC 2021, The Fourteenth International Conference on Advances in Human-oriented and Personalized Mechanisms, Technologies, and Services
  • VALID 2021, The Thirteenth International Conference on Advances in System Testing and Validation Lifecycle
  • SIMUL 2021, The Thirteenth International Conference on Advances in System Simulation
  • SOTICS 2021, The Eleventh International Conference on Social Media Technologies, Communication, and Informatics
  • INNOV 2021, The Tenth International Conference on Communications, Computation, Networks and Technologies
  • HEALTHINFO 2021, The Sixth International Conference on Informatics and Assistive Technologies for Health-Care, Medical Support and Wellbeing

NetWare 2021 Congress
November 14, 2021 to November 18, 2021 - Athens, Greece

  • SENSORCOMM 2021, The Fifteenth International Conference on Sensor Technologies and Applications
  • SENSORDEVICES 2021, The Twelfth International Conference on Sensor Device Technologies and Applications
  • SECURWARE 2021, The Fifteenth International Conference on Emerging Security Information, Systems and Technologies
  • AFIN 2021, The Thirteenth International Conference on Advances in Future Internet
  • CENICS 2021, The Fourteenth International Conference on Advances in Circuits, Electronics and Micro-electronics
  • ICQNM 2021, The Fifteenth International Conference on Quantum, Nano/Bio, and Micro Technologies
  • FASSI 2021, The Seventh International Conference on Fundamentals and Advances in Software Systems Integration
  • GREEN 2021, The Sixth International Conference on Green Communications, Computing and Technologies

TrendNews 2021 Congress
November 14, 2021 to November 18, 2021 - Athens, Greece

  • CORETA 2021, Advances on Core Technologies and Applications
  • DIGITAL 2021, Advances on Societal Digital Transformation

 


ThinkMind // International Journal On Advances in Life Sciences, volume 5, numbers 3 and 4, 2013 // View article lifsci_v5_n34_2013_5


Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters

Authors:
Ondrej Strnad
Barbora Kozlikova
Vilem Sustr
Jiri Sochor

Keywords: protein, empty space, void, visualization, real-time, cavity, volume, Voronoi diagram, Delaunay triangulation

Abstract:
Long-term research in the area of protein analysis proved the importance of an empty space situated inside these macromolecular structures. This empty space influences the protein function, characteristics or reactivity. Many algorithms enabling computation of these empty spaces (or voids) have been published and their results were evaluated by protein engineers to confirm their chemical relevance. However, not all detected voids inside protein are of the same importance. Thus, the examination and assessment of all voids must follow to reveal the important ones. In this phase the visual representation of voids is very valuable and substantially decreases the time spent in this evaluation phase. In this paper we present an extension of the algorithm for the visualization and further evaluation of protein voids in real-time. The user-driven approach enables to compute and display empty space that satisfies the input parameters instantly. The values of these parameters can be changed by the user anytime and the changes are immediately displayed and prepared for further exploration. Our improvements involve an exclusion of selected atom or group of atoms (ligands, ions) from the computation, which can change the size and shape of the detected void. Another improvement is related to the detection of the binding site which is usually located in one of the largest voids. So the algorithm suggests and visually separates (by different coloring) the largest void of given area. Several improvements were also made in the field of real-time exploration – currently the interaction on large structures is fluent. In consequence, the current version of the algorithm provides the biochemists with very adjustable and precise algorithm for detection of inner voids in a user-defined region of protein structures.

Pages: 160 to 170

Copyright: Copyright (c) to authors, 2013. Used with permission.

Publication date: December 31, 2013

Published in: journal

ISSN: 1942-2660

SERVICES CONTACT
2010 - 2017 © ThinkMind. All rights reserved.
Read Terms of Service and Privacy Policy.