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조영송(Youngsong Cho),김재관(Jae-Kwan Kim),유중현(Joonghyun Ryu),이목원(Mokwon Lee),차제현(Jehyun Cha),송찬영(Chanyoung Song),김덕수(Deok-Soo Kim) (사)한국CDE학회 2014 한국 CAD/CAM 학회 학술발표회 논문집 Vol.2014 No.8
Geometric properties are critical for the function of molecules consisting of atoms with different radii which are usually modeled as spheres in 3D. “Molecular Geometry” is a theoretical framework of computational understanding of the geometry of molecules in the claim that most molecular structure problems can be effectively and efficiently facilitated by the “geometrization” of the problem into that among spheres in 3D whose solution can be easily found via “geometry kernel”. In this paper, we report BULL!, the molecular geometry engine based on the Voronoi diagram of spheres, the quasi-triangulation, and the beta-complex. Being a program implemented in C++, application programmers can simply call API-functions of BULL! to create application programs correctly, efficiently, and conveniently. The BULL! is designed compatibly so that application programs are completely independent of future modifications and improvements. The BULL! engine will be freely available from the Voronoi Diagram Research Center at Hanyang University.
An efficient algorithm for computing the area of a molecular surface using β-complex
Joonghyun Ryu(유중현),Youngsong Cho(조영송),Donguk Kim(김동욱),Jeongyeon Seo(서정연),Deok-Soo Kim(김덕수) 대한산업공학회 2008 대한산업공학회 춘계학술대회논문집 Vol.2008 No.5
It is well known that the structure of a protein mostly determines the function of a protein. Hence, the structure of a protein is very important for studying the function of a protein. A molecular surface of a protein is one of the important structures for a protein. The area of a molecular surface is critically related with protein docking and protein folding through solvation energy. This paper presents an algorithm for computing the area of a molecular surface precisely and efficiently based on a β-complex. Given a β-complex of a protein, the algorithm can compute the area of a molecular surface in O(n) time in the worst case where n is the number of atoms in the protein.
An efficient algorithm for computing the area of a molecular surface using β-complex
Joonghyun Ryu(유중현),Youngsong Cho(조영송),Donguk Kim(김동욱),Jeongyeon Seo(서정연),Deok-Soo Kim(김덕수) 한국경영과학회 2008 한국경영과학회 학술대회논문집 Vol.2008 No.5
It is well known that the structure of a protein mostly determines the function of a protein. Hence, the structure of a protein is very important for studying the function of a protein. A molecular surface of a protein is one of the important structures for a protein. The area of a molecular surface is critically related with protein docking and protein folding through solvation energy. This paper presents an algorithm for computing the area of a molecular surface precisely and efficiently based on a β-complex. Given a β-complex of a protein, the algorithm can compute the area of a molecular surface in O(n) time in the worst case where n is the number of atoms in the protein.