The KIPS Transactions:PartB (정보처리학회논문지B)

Korea Information Processing Society (한국정보처리학회)
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A Study of Flexible Protein Structure Alignment Using Three Dimensional Local Similarities

단백질 3차원 구조의 지역적 유사성을 이용한 Flexible 단백질 구조 정렬에 관한 연구

  • 박찬용 (한국전자통신연구원 라이프인포매틱스팀) ;
  • 황치정 (충남대학교 전기정보통신공학부)
  • Published : 2009.10.31
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Abstract

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.

구조적 생물 정보학 분야는 단백질의 3차원 구조를 대상으로 단백질을 연구하는 분야이며, 본 논문에서는 구조적 생물 정보학 분야의 핵심 연구 주제중의 하나인 Flexible 단백질 구조 정렬에 관한 새로운 알고리즘을 제시한다. Flexible 단백질 구조 정렬을 위하여, 단백질의 3차원 구조의 지역적인 유사성을 이용하여 두 단백질의 유사한 부분 구조를 추출해 내고, 이 추출된 유사 구조간에 연결 가능성을 검색하여 정렬이 가능한 모든 유사 구조를 찾고, 이 유사 구조에 꺽임점을 도입하여 Flexible 단백질 구조 정렬을 수행하였다. 이 과정에서 단백질의 지역적 유사성을 정확히 비교하기 위하여 RDA를 이용한 방법을 제안하였고, Flexible 단백질 구조 정렬시 신뢰성 있는 꺽임점 위치 선정 방법과 그래프를 이용한 최적화 방법을 제안하였다. 성능 평가를 위하여 다양한 방법으로 Flexible 단백질 구조 정렬의 성능 평가를 수행하였고, 기존의 방법인 DALI, CE, FATCAT 보다 성능의 우수함을 나타내었다.

Keywords

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