Frontiers of Mechanical Engineering >

2013 , Vol. 8 >Issue 1: 104 - 108

DOI: https://doi.org/10.1007/s11465-013-0360-9

RESEARCH ARTICLE

Computation of the protein molecular mechanism using adaptive dihedral angle increments

  • Mikel DIEZ ,
  • Victor PETUYA ,
  • Mónica URIZAR ,
  • Erik MACHO ,
  • Oscar ALTUZARRRA
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  • Department of Mechanical Engineering, University of the Basque Country UPV/EHU, Bizkaia 48013, Spain

Received date: 08 Nov 2012

Accepted date: 13 Dec 2012

Published date: 05 Mar 2013

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg
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Abstract

Protein motion simulation is still a troublesome problem yet to be solved, especially due to its high computational requirements. The procedure presented in this paper makes use of the proteins’ real degrees of freedom (DOFs). The procedure makes no use of any intermediate energy minimization processes that may alter the motion path or result in very high computational cost requirements. In order to reduce the computational cost, presented algorithms make use of the balls and rods approach for protein structure modelization. Also, structures are normalized in order to minimize inaccuracies introduced by experimental methods, providing a more efficient but still accurate structure for motion simulation.

Key words： kinematics; serial robot; proteins; folding; molecular mechanism

Cite this article

Mikel DIEZ , Victor PETUYA , Mónica URIZAR , Erik MACHO , Oscar ALTUZARRRA . Computation of the protein molecular mechanism using adaptive dihedral angle increments[J]. Frontiers of Mechanical Engineering, 2013 , 8(1) : 104 -108 . DOI: 10.1007/s11465-013-0360-9

Acknowledgements

The authors wish to acknowledge the financial support received from the Spanish Government through the Ministerio de Economía y Competitividad (Project DPI2011-22955), the European Union (Project FP7-CIP-ICT-PSP-2009-3) and the Regional Government of the Basque Country through the Departamento de Educación, Universidades e Investigación (Project IT445-10) and UPV/EHU underβprogram UFI 11/29.

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