A robotics approach to enhance conformational sampling of proteins

Juan C. Cortés, Ibrahim Al-Bluwi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2012
Pages1177-1186
Number of pages10
EditionPARTS A AND B
DOIs
StatePublished - Dec 1 2012
Externally publishedYes
EventASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2012 - Chicago, IL, United States
Duration: Aug 12 2012Aug 12 2012

Publication series

NameProceedings of the ASME Design Engineering Technical Conference
NumberPARTS A AND B
Volume4

Conference

ConferenceASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2012
CountryUnited States
CityChicago, IL
Period8/12/128/12/12

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Mechanical Engineering
  • Computer Science Applications
  • Computer Graphics and Computer-Aided Design

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  • Cite this

    Cortés, J. C., & Al-Bluwi, I. (2012). A robotics approach to enhance conformational sampling of proteins. In ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2012 (PARTS A AND B ed., pp. 1177-1186). (Proceedings of the ASME Design Engineering Technical Conference; Vol. 4, No. PARTS A AND B). https://doi.org/10.1115/DETC2012-70105