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Side Chain Kinematics Simulation on Protein Conformational Changes

  • Mikel DiezEmail author
  • Victor Petuya
  • Mónica Urizar
  • Oscar Altuzarra
  • Alfonso Hernández
Part of the Mechanisms and Machine Science book series (Mechan. Machine Science, volume 30)

Abstract

Protein simulation remains as one of the most difficult task for biologists, physicists or engineers. The huge computational requirements of the protein models makes it difficult to obtain simulations of big conformational changes on protein structure. Side chain modelization is a critical step when obtaining the protein structure model. The time scale at which side chain movement occur can greatly increase the computational cost of the process. In this paper, we propose a side chain orientation procedure with a very low computational cost. This procedure has been implemented in combination with other procedures to obtain a computationally efficient simulation tool for protein simulation. This simulation tool has been used to simulate several protein conformational changes with success.

Keywords

Protein Side chains Simulation 

Notes

Acknowledgments

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

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Mikel Diez
    • 1
    Email author
  • Victor Petuya
    • 1
  • Mónica Urizar
    • 1
  • Oscar Altuzarra
    • 1
  • Alfonso Hernández
    • 1
  1. 1.Department of Mechanical EngineeringUniversity of the Basque Country UPV/EHUBilbaoSpain

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