Incorporating the Depth and Protrusion Index in the Protein Ray Based Descriptor
One of the most popular issues in bioinformatics community nowadays is determination of protein function. In order to achieve that, efficient protein tertiary structure retrieval methods should be provided. The necessity of accurate, robust and efficient algorithms for protein tertiary structure retrieval is even more obvious as the number of known protein structures rapidly increases. In this paper we incorporate several features in the protein ray based descriptor in order to provide more accurate protein tertiary structure retrieval. First, the protein backbone is uniformly interpolated. Then, for each of the interpolation points, beside the Euclidean distance from the interpolation point to the center of mass, the accessible surface area (ASA), relative ASA (RASA), depth index, protrusion index and hydrophobicity of the nearest amino-acid are extracted and incorporated in the descriptor. The experimental results showed that by incorporating these features, higher precision (more than 2％ improvement) is achieved than by using the Euclidean distance as a single feature.
Protein structure retrieval protein tertiary structure, protein ray based descriptor ASA RASA depth index protrusion index hydrophobicity
Georgina Mirceva Danco Davcev
Computer Science and Engineering Department Ss. Cyril and Methodius University in Skopje, Faculty of Electrical Engineering and Information Technologies Skopje, Macedonia
国际会议
上海
英文
1640-1644
2011-07-26（万方平台首次上网日期，不代表论文的发表时间）