Ku-Jin Kim

KIPS Transactions on Software and Data Engineering, Vol. 8, No. 10, pp. 421-426, Oct. 2019
https://doi.org/10.3745/KTSDE.2019.8.10.421,   PDF Download:
Keywords: Protein Contact Region, Molecular Surface, Binding Interface, Geometric Feature, Mean Curvature
Abstract

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.

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