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Molecules 2017, 22(10), 1722; doi:10.3390/molecules22101722

Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions

1
School of Life Sciences and Biotechnology, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea
2
Department of Information Technology, Anna University Regional Campus, Coimbatore 641046, Tamil Nadu, India
3
School of Computer Science and Engineering, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea
*
Author to whom correspondence should be addressed.
Received: 31 August 2017 / Revised: 6 October 2017 / Accepted: 12 October 2017 / Published: 13 October 2017
(This article belongs to the Special Issue Protein-Protein Interactions)
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Abstract

Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction. View Full-Text
Keywords: protein-protein interface; contact area; binding direction; protein docking protein-protein interface; contact area; binding direction; protein docking
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Kang, B.S.; Pugalendhi, G.; Kim, K.-J. Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions. Molecules 2017, 22, 1722.

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