Abstract

Recent researches have clarified that the function of protein depends on its molecular surface. They suggest the possibility of the protein function identification based on the molecular surface comparison, in which a molecular surface of an unknown protein is compared with many surfaces of known active sites as reference templates. This paper presents an effective surface comparison method by using normal vectors with attributes of the curvature and the physical properties on projections and depressions. The vectors that should be matched are limited by extracting two vectors at similar relative positions and with the attributes of surface in order to reduce computational complexity. The proposed method was applied to 11 surface data. As a result, the mean calculation time was about 3 min, and it was possible to compare at approximately an optimal location. This method was applied to 103 surface data. The result of identification showed 95.2% identification accuracy.

Author Keywords: Protein; Active site; Molecular surface comparison; Protein function identification; Normal vector

Article Outline

1. Introduction

2. Protein molecular surface and comparison

2.1. Molecular surface data

2.2. The comparison of molecular surface

3. Method of comparing protein molecular surface

3.1. Approach

3.2. Overview of the method

3.3. Creating normal vectors with attributes

3.3.1. Mean curvature and Gaussian curvature

3.3.2. A method of creating the normal vectors with attributes

3.4. Efficient matching by normal vectors with attributes

3.4.1. Efficient matching by the bucket method

3.4.2. Efficient matching by threshold

3.5. Improving matched position by local search method

4. Evaluation

4.1. Evaluation of matching efficiency and accuracy

4.2. Evaluation of accuracy of function identification

5. Conclusion

Acknowledgements

References