Side Chain Kinematics Simulation on Protein Conformational Changes
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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.
KeywordsProtein Side chains Simulation
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.
- Bohnenkamp P, Kazerounian K, Ilies HT (2007) Structural prediction of peptide based nano systems via progressive landscape evolution. In: Proceedings 12th IFToMM world congress, Besancon, France, pp 1–6Google Scholar
- Diez M, Petuya V, Martínez I, Hernandez A (2013) Protein secondary structure detection using dihedral angle parameters evaluation. In: Proceedings of SYROM 2013, Brasov, Romania, pp 127–134Google Scholar
- Kavraki LE (2007) Protein-ligand docking, including flexible receptor-flexible ligand docking. OpenStax CNX. Mar 22 2007. http://cnx.org/contents/4e7287b0-6c38-4829-abeb-3ae357bbf60f@10@10