Contact Curve Based Simulation of Side Chains from Two Amino Acids in a Protein Molecule

Authors

  • Sanghun Jeong School of Computer Science and Engineering, Kyungpook National University, Korea. Software Technology Research Center (SWRC), Kyungpook National University, Korea.
  • Ku-Jin Kim School of Computer Science and Engineering, Kyungpook National University, Korea. Software Technology Research Center (SWRC), Kyungpook National University, Korea.

Keywords:

Protein Molecule, Side Chain Flexibility, Collision Detection,

Abstract

In this paper, an algorithm to compute the contact configuration between the rotating side chains from two amino acids in a protein molecule is proposed. The main chain and side chain parts in one amino acid are considered as two rigidbody parts combined with a revolute joint. While the atom positions in the main chain parts of two amino acids are fixed, the side chains possibly rotate, which can cause the collision between amino acids. On the plane of rotation angle parameters, we find the region for two side chains colliding each other. Then, by extracting the boundary of the region, the contact curve of the amino acids is found, where by using it, the amino acids with rotating side chains can be simulated.

References

M. Diez, V. Petuya, L. A. Martinez-Cruz, A. Hernandez, Insights into mechanism kinematics for protein motion simulation, BMC Bioinformatics, 15(184) (2014).

B. Gipson, D. Hsu, L. E. Kavraki, J.-C. Latombe, Computational Models of Protein Kinematics and Dynamics: Beyond Simulation, Annu. Rev. Anal. Chem., 5 (2012) 273-291.

W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Computer simulation of biomolecular systems: theoretical and experimental applications, Vol. 3. Springer Science & Business Media (2013).

A. Bondi, van der Waals volumes and radii, The Journal of physical chemistry, 68(3) (1964) 441-451.

G. E. Schulz and R. H. Schirmer, Principles of protein structure, Springer Science & Business Media (2013).

K. –J. Kim, E. Sacks, L. Joskowicz, Kinematic analysis of spatial fixed-axis higher pairs using configuration spaces, Computer-Aided Design 35(3) (2003) 279-291.

Downloads

Published

2017-06-01

How to Cite

Jeong, S., & Kim, K.-J. (2017). Contact Curve Based Simulation of Side Chains from Two Amino Acids in a Protein Molecule. Journal of Telecommunication, Electronic and Computer Engineering (JTEC), 9(2-6), 91–94. Retrieved from https://jtec.utem.edu.my/jtec/article/view/2443

Issue

Vol. 9 No. 2-6: Circuit and System Advancement in Modern World V

Section

Articles

License

TRANSFER OF COPYRIGHT AGREEMENT

The manuscript is herewith submitted for publication in the Journal of Telecommunication, Electronic and Computer Engineering (JTEC). It has not been published before, and it is not under consideration for publication in any other journals. It contains no material that is scandalous, obscene, libelous or otherwise contrary to law. When the manuscript is accepted for publication, I, as the author, hereby agree to transfer to JTEC, all rights including those pertaining to electronic forms and transmissions, under existing copyright laws, except for the following, which the author(s) specifically retain(s):

  1. All proprietary right other than copyright, such as patent rights
  2. The right to make further copies of all or part of the published article for my use in classroom teaching
  3. The right to reuse all or part of this manuscript in a compilation of my own works or in a textbook of which I am the author; and
  4. The right to make copies of the published work for internal distribution within the institution that employs me

I agree that copies made under these circumstances will continue to carry the copyright notice that appears in the original published work. I agree to inform my co-authors, if any, of the above terms. I certify that I have obtained written permission for the use of text, tables, and/or illustrations from any copyrighted source(s), and I agree to supply such written permission(s) to JTEC upon request.