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A Robotics Approach to Enhance Conformational Sampling of Proteins

[+] Author Affiliations
Juan Cortés, Ibrahim Al-Bluwi

LAAS-CNRS, Toulouse, France

Paper No. DETC2012-70105, pp. 1177-1186; 10 pages
doi:10.1115/DETC2012-70105
From:
  • ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 4: 36th Mechanisms and Robotics Conference, Parts A and B
  • Chicago, Illinois, USA, August 12–15, 2012
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-4503-5
  • Copyright © 2012 by ASME

abstract

Proteins are biological macromolecules that play essential roles in living organisms. Furthermore, the study of proteins and their function is of interest in other fields in addition to biology, such as pharmacology and biotechnology. Understanding the relationship between protein structure, dynamics and function is indispensable for advances in all these areas. This requires a combination of experimental and computational methods, whose development is the object of very active interdisciplinary research. In such a context, this paper presents a technique to enhance conformational sampling of proteins carried out with computational methods such as molecular dynamics simulations or Monte Carlo methods. Our approach is based on a mechanistic representation of proteins that enables the application of efficient methods originating from robotics. The paper explains the generalities of the approach, and gives details on its application to devise Monte Carlo move classes. Results show the good performance of the method for sampling the conformational space of different types of proteins.

Copyright © 2012 by ASME
Topics: Robotics , Proteins

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