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MCL 알고리즘을 이용한 단백질 표면의 바인딩 영역 분석 기법
정광수,유기진,정용제,류근호,Jung, Kwang-Su,Yu, Ki-Jin,Chung, Yong-Je,Ryu, Keun-Ho 한국정보처리학회 2007 정보처리학회논문지D Vol.14 No.7
단백질은 다른 물질과의 결합하여 기능을 수행하기 때문에 활성 사이트가 유사한 단백질은 유사한 기능을 가진다. 따라서 단백질의 바인딩 영역을 식별함으로써 단백질의 기능을 추론할 수 있다. 이 논문은 MCL (Markov Cluster) 알고리즘을 이용하여 단백질의 바인딩 영역을 추출하는 새로운 방법을 제시한다. 이를 위하여 단백질의 표면 잔기 거리를 나타내는 distance matrix를 생성하고, 여기에 MCL 프로세스를 적용한다. 제시한 방법을 평가하기 위해 Catalytic Site Atlas (CSA) 데이터를 사용하였다. CSA 데이터 (94개의 단일 체인 단백질)를 이용한 실험 결과, 알고리즘은 91개 단백질의 활성 사이트 주변의 바인딩 영역을 검출하였다. 이 논문은 단백질 활성 사이트를 분석하기 위한 새로운 기하학적 특징을 제시하였고, 활성 사이트와 관련이 없는 잔기를 제거함으로써 단백질 표면의 분석의 시간을 줄일 수 있는 장점이 있다. Proteins combine with other materials to achieve their function and have similar function if their active sites are similar. Thus we can infer the function of protein by identifying the binding area of proteins. This paper suggests the novel method to select binding area of protein using MCL (Markov Cluster) algorithm. We construct the distance matrix from surface residues distance on protein. Then this distance matrix is transformed to connectivity matrix for applying MCL process. We adopted Catalytic Site Atlas (CSA) data to evaluate the proposed method. In the experimental result using CSA data (94 selected single chain proteins), our algorithm detects the 91 (97%) binding area near by active site of each protein. We introduced a new geometrical features and this mainly contributes to reduce the time to analyze the protein by selecting the residues near by active site.
정광수 ( Kwang Soo Chung ) 안암법학회 2008 안암 법학 Vol.0 No.27
If the liability to compensation for demage in the process of negotiating a contract incurred is able to be accepted, it concerns Culpa in Contrahendo. Culpa in Contrahendo is known to be derived from certain unique features of the German Civil Code. Because German tort statutes(§§823, 826 etc.) do not cover the pure property loss, the pure property loss which is incurred in the process of negotiating a contract shall be subject to the contract liability(=Culpa in Contrahendo). On the other hand, the Korean Civil Code §750(tort statute) covers the pure property. Therefore, A minority opinion is that there is no need to introduce the theory of Culpa in Contrahendo to the Korean Civil Code. However I can`t assent to the opinion of the minority. I clarify my position for several reasons. First, though the tort statute of Swiss Civil Code and the tort statute of Austrian Civil Code are general clauses as well as the tort statute of Korean Civil Code, all of these countries recognize Culpa in Contrahendo. Second, my position is related to the theory of old civil suit-object and the disposal of parties to the civil suit in Korea. Third, §535(Culpa in Contrahendo) of Korean Civil Code provides that the liability to compensate for loss is assumed when a party of contract is aware of the fact that a contract of initial impossibility is invalid or when the party is in a position to recognize the fact. So we are of the view that there are needs to interpretate by analogy of §535(Culpa in Contrahendo statute) and apply the statute to the liability to compensation for demage in the process of negotiating a contract incurred. In Conclusion, I must insist on this fact that Culpa in Contrahendo is a similar contract liability native to statute(§535 of Korean Civil Code) in Korea.