Open Access

ARTICLE

Orienting a Protein Model by Crossing Number to Generate the Characteristic Views for Identification

Chikit Au¹, Yiyu Cai², Jianmin Zheng³, Tony Woo⁴

1 Department of Engineering, University of Waikato, New Zealand. E-mail: ckau@waikato.ac.nz
2 School of Mechanical Engineering, Nanyang Technological University, Singapore
3 School of Computer Engineering, Nanyang Technological University, Singapore
4 School of Mechanical Engineering, Nanyang Technological University, Singapore

Computer Modeling in Engineering & Sciences 2010, 68(3), 221-238. https://doi.org/10.3970/cmes.2010.068.221

Abstract

A protein model (such as a ribbon model) can be created from the atomic coordinates in the protein data base files. These coordinates are obtained by X-ray crystallography or NMR spectroscopy with the protein arbitrarily oriented. As such, identifying or comparing a novel structure with a known item using protein model in the protein data base can be a timely process since a large number of transformations may be involved. The identification efficiency will be improved if the protein models are uniformly oriented. This paper presents an approach to orient a protein model to generate the characteristic views with minimum and maximum crossings respectively. The projection directions for these characteristic views are determined by a set of crossing maps (C-maps). Re-orientating the protein models in the protein data base to two characteristic views will facilitate the process of identification.

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Keywords

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