An Algorithm for Computing Valid Side Chain Conformations for Finding Transformed Channels in a Protein Molecule


KIPS Transactions on Computer and Communication Systems, Vol. 4, No. 1, pp. 1-4, Jan. 2015
10.3745/KTCCS.2015.4.1.1,   PDF Download:

Abstract

This paper presents an algorithm for finding valid side chain conformations of amino acids, when given channel is transformed. The suggested algorithm implements a protein molecule with flexible side chains based on the flexibility of amino acids, and extracts adjacent amino acids that affect the formation of the channel. We detect the collision between adjacent amino acids and neighbors, in order to exclude invalid side chain conformations. Then, we construct the rotation angle combination tree to choose valid side chain conformations.


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Cite this article
[IEEE Style]
J. H. Choi, B. J. Kim, K. J. Kim, "An Algorithm for Computing Valid Side Chain Conformations for Finding Transformed Channels in a Protein Molecule," KIPS Transactions on Computer and Communication Systems, vol. 4, no. 1, pp. 1-4, 2015. DOI: 10.3745/KTCCS.2015.4.1.1.

[ACM Style]
Ji Hoon Choi, Byung Joo Kim, and Ku Jin Kim. 2015. An Algorithm for Computing Valid Side Chain Conformations for Finding Transformed Channels in a Protein Molecule. KIPS Transactions on Computer and Communication Systems, 4, 1, (2015), 1-4. DOI: 10.3745/KTCCS.2015.4.1.1.