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단백질의 도메인-도메인 간 상호작용 원자들의 밀도 분포 분석
원정인(Chung-In Won),김정민(Chong-Min Kim),조영송(Youngsong Cho),김동욱(Donguk kim),박종화(Jong Bhak),김덕수(Deok-Soo Kim) 대한산업공학회 2008 대한산업공학회 춘계학술대회논문집 Vol.2008 No.5
The packing density of atoms constituting a protein has been studied as an important measure of protein structures to solve the problems such as docking and folding. Especially, the packing density of domain which is a separated subsection participating in function of the protein plays an essential role for understanding the cellular process. To calculate the packing density, it is important to calculate the precise volume of atomic region. The Voronoi diagram of atoms calculates volume of atomic region precisely with an atomic character and no computational errors, not like the previous methods. In this paper, the packing density of atoms constituting domain-domain interface was calculated via the Voronoi diagram of atoms and their distributions are analyzed.
단백질의 도메인-도메인 간 상호작용 원자들의 밀도 분포 분석
원정인(Chung-In Won),김정민(Chong-Min Kim),조영송(Youngsong Cho),김동욱(Donguk kim),박종화(Jong Bhak),김덕수(Deok-Soo Kim) 한국경영과학회 2008 한국경영과학회 학술대회논문집 Vol.2008 No.5
The packing density of atoms constituting a protein has been studied as an important measure of protein structures to solve the problems such as docking and folding. Especially, the packing density of domain which is a separated subsection participating in function of the protein plays an essential role for understanding the cellular process. To calculate the packing density, it is important to calculate the precise volume of atomic region. The Voronoi diagram of atoms calculates volume of atomic region precisely with an atomic character and no computational errors, not like the previous methods. In this paper, the packing density of atoms constituting domain-domain interface was calculated via the Voronoi diagram of atoms and their distributions are analyzed.
단백질의 sphericity measure를 결정하는 β-probe 크기의 통계적 분석
김재관(Jae-Kwan Kim),원정인(Chung-In Won),조영송(Youngsong Cho),배석주(Sukjoo Bae),박종화(Jong Bhak),김덕수(Deok-Soo Kim) 대한산업공학회 2008 대한산업공학회 춘계학술대회논문집 Vol.2008 No.5
Organism consists of molecules. Among others, proteins are considered one of the most important units of life. Protein consists of amino acids and amino acids consists of atoms. The structure of a protein is important. Due to the general consensus of the importance of morphological structure to its functions, many studies have been performed to understand the threedimensional geometric structure of a protein. Therefore, it is believed that a simple parameter for the overall shape descriptor of a protein will be convenient if it can be easily defined and computed. In this paper, we will present a quantitative measure for the sphericity of protein based on a computational geometric construct called the betacomplex. The parameter thus obtained is determined via a statistical analysis of computed sphericity from sample set of protein structures. This paper then presents an statistical approach to determine the best parameter for the sphericity.
단백질의 sphericity measure를 결정하는 β-probe 크기의 통계적 분석
김재관(Jae-Kwan Kim),원정인(Chung-In Won),조영송(Youngsong Cho),배석주(Sukjoo Bae),박종화(Jong Bhak),김덕수(Deok-Soo Kim) 한국경영과학회 2008 한국경영과학회 학술대회논문집 Vol.2008 No.5
Organism consists of molecules. Among others, proteins are considered one of the most important units of life. Protein consists of amino acids and amino acids consists of atoms. The structure of a protein is important. Due to the general consensus of the importance of morphological structure to its functions, many studies have been performed to understand the threedimensional geometric structure of a protein. Therefore, it is believed that a simple parameter for the overall shape descriptor of a protein will be convenient if it can be easily defined and computed. In this paper, we will present a quantitative measure for the sphericity of protein based on a computational geometric construct called the betacomplex. The parameter thus obtained is determined via a statistical analysis of computed sphericity from sample set of protein structures. This paper then presents an statistical approach to determine the best parameter for the sphericity.
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.
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.
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.