Incorporating several features in the protein ray descriptor for more accurate protein 3D structure retrieval

Authors:
Georgina Mirceva;Danco Davcev
Affiliations:
Ss. Cyril and Methodius University, Faculty of Electrical Engineering and Information Technologies, Skopje, Macedonia;Ss. Cyril and Methodius University, Faculty of Electrical Engineering and Information Technologies, Skopje, Macedonia
Venue:
Proceedings of the ACM workshop on 3D object retrieval
Year:
2010

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Efficient protein tertiary structure retrievals and classifications using content based comparison algorithms

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Abstract

The retrieval of protein structures is one of the most popular topics in bioinformatics community nowadays, since it can be further used for determining protein function. With the technology innovation, the number of protein tertiary structures increases every day, so the necessity of accurate, robust and efficient algorithms for protein 3D structure retrieval arises. In this paper we improve the ray based descriptor, in sense of achieving higher precision. First, the protein backbone is uniformly interpolated, as in the process of extraction of the existing protein ray based descriptor. Then, for each of the approximation points, beside the Euclidean distance from the point to the centre of mass, the ASA, RASA and hydrophobicity of the nearest amino acid are extracted and added to the descriptor. The analysis showed that by incorporating these features, we achieve higher precision (2.26% improvement) than by using only the Euclidean distance as a single feature.