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Protein-Ligand Docking: an Approach Based on β-shape and Heuristics
Chong-Min Kim(김정민),Junghyun Ryu(유중현),Chung-In Won(원정인),Jong Bhak(박종화),Deok-Soo Kim(김덕수) 한국경영과학회 2008 한국경영과학회 학술대회논문집 Vol.2008 No.5
Protein-ligand docking has been known to be very important for the development of new drugs. Protein-ligand docking problem is to search the best fit region between a protein and a ligand, and heuristic algorithms such as genetic algorithm and simulated annealing have been used for the searching method. Finding the Initial position of ligand to perform the searching method is important and our approach is based on the geometric construct called a β-shape which represents the proximity among atoms on the surface of the protein. In this paper, we show the use of β-shape for the initial solutions of genetic algorithm and simulated annealing methods applied for protein-ligand docking problem.
Protein-Ligand Docking: an Approach Based on β-shape and Heuristics
Chong-Min Kim(김정민),Junghyun Ryu(유중현),Chung-In Won(원정인),Jong Bhak(박종화),Deok-Soo Kim(김덕수) 대한산업공학회 2008 대한산업공학회 춘계학술대회논문집 Vol.2008 No.5
Protein-ligand docking has been known to be very important for the development of new drugs. Protein-ligand docking problem is to search the best fit region between a protein and a ligand, and heuristic algorithms such as genetic algorithm and simulated annealing have been used for the searching method. Finding the Initial position of ligand to perform the searching method is important and our approach is based on the geometric construct called a β-shape which represents the proximity among atoms on the surface of the protein. In this paper, we show the use of β-shape for the initial solutions of genetic algorithm and simulated annealing methods applied for protein-ligand docking problem.
단백질-리간드 결합의 유전알고리듬을 위한 β-shape 기반의 초기 모집단
김정민(Chong-Min Kim),유중현(Junghyun Ryu),원정인(Chung-In Won),이창희(Changhee Lee),김재관(Jae-Kwan Kim),박종화(Jong Bhak),김덕수(Deok-Soo Kim) 대한산업공학회 2008 대한산업공학회 추계학술대회논문집 Vol.2008 No.11
Protein-ligand docking has been known to be essential for the development of new drugs. Proteinligand docking problem is to search the best region to fit between a protein and a ligand and this problem is very complicated that the number of possible conformations is astronomically thousands. Hence, genetic algorithm is widely used for the searching method in protein-ligand docking problem. Generally, a chromosome is modeled as a position of the ligand, and we created initial population by using a pocket extracted via β-shape. In this research, we show the better performance of genetic algorithm for protein-ligand docking than prior works.
Computation of Volume of Molecular Surface Using β-Complex
Jeongyeon Seo(서정연),Youngsong Cho(조영송),Junghyun Ryu(유중현),Deok-Soo Kim(김덕수) 대한산업공학회 2008 대한산업공학회 춘계학술대회논문집 Vol.2008 No.5
Molecular surface of a protein is one of the most important geometric structures of the protein. Given a molecular surface, various molecular properties such as the area, volume, and density of a protein can be defined. Especially, the volume among the molecular properties is one of the fundamental properties for studying protein docking and folding. This paper presents an efficient and precise algorithm to compute the volume bounded by the molecular surface. It is based on β-complex which is an efficient data structure reflected the size difference among atoms of the protein in Euclidean metric.
Computation of Volume of Molecular Surface Using β-Complex
Jeongyeon Seo(서정연),Youngsong Cho(조영송),Junghyun Ryu(유중현),Deok-Soo Kim(김덕수) 한국경영과학회 2008 한국경영과학회 학술대회논문집 Vol.2008 No.5
Molecular surface of a protein is one of the most important geometric structures of the protein. Given a molecular surface, various molecular properties such as the area, volume, and density of a protein can be defined. Especially, the volume among the molecular properties is one of the fundamental properties for studying protein docking and folding. This paper presents an efficient and precise algorithm to compute the volume bounded by the molecular surface. It is based on β-complex which is an efficient data structure reflected the size difference among atoms of the protein in Euclidean metric.