Joonghyun Ryu | Hanyang University (original) (raw)

Papers by Joonghyun Ryu

Abstract. Protein consists of amino acids, and an amino acid consists of atoms. Given a protein, ... more Abstract. Protein consists of amino acids, and an amino acid consists of atoms. Given a protein, understanding its functions is critical for vari-ous reasons for designing new drugs, treating diseases, and so on. Due to recent researches, it is now known that the structure of ...

Journal of Zhejiang University Science, 2006

Pockets in proteins have been known to be very important for the life process. There have been se... more Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.

ABSTRACT In recent years, there have been extensive studies on biological systems such as protein... more ABSTRACT In recent years, there have been extensive studies on biological systems such as proteins. Being one of the most important aspects, the geometry has been more important since the morphology of a molecular system is known to determine the critical functions of the molecule. In the study of the shape and the structure of a molecule, the representation of proximity information among atoms in the molecule is the most fundamental research issue. In this paper, we present a ?-shape and a ?-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known a-shape and a- complex (and their weighted counterparts as well). To compute a ?-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasitriangulation which is the topological dual of the Voronoi diagram. Then, we compute a ?-complex from the quasitriangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a ?-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a ?-shape for a particular ? consisting of k simplices can be located O(logm + k) time in the worst case from the simplicies in the ?-complex sorted according to the interval values.

Advanced Functional Materials, 2010

Journal of Biomolecular Structure & Dynamics, 2011

This paper presents an approach and a software, BetaDock, to the docking problem by putting the p... more This paper presents an approach and a software, BetaDock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the β-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the β-complex corresponding to water molecule is computed. Then, the boundary of the β-complex defines the β-shape which has the complete proximity information among all atoms on the receptor boundary. From the β-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that BetaDock is superior to a popular docking software AutoDock 4.

Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defi... more Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defined with respect to a probe approximating a solvent molecule. This paper presents an efficient, as efficient as the realtime, algorithm to triangulate the blending surfaces which is the most critical subset of a molecular surface. For the quick evaluation of points on the surface, the proposed algorithm uses masks which are similar in their concepts to those in subdivision surfaces. More fundamentally, the proposed algorithm takes advantage of the concise representation of topology among atoms stored in the β-shape which is indeed used in the computation of the blending surface itself. Given blending surfaces and the corresponding β-shape, the proposed algorithm triangulates the blending surfaces in O(c · m) time in the worst case, where m is the number of boundary atoms in the protein and c is the number of point evaluations on a patch in the blending surface.

Summary. The topology among particles frequently plays a core role in many appli-cations. One of ... more Summary. The topology among particles frequently plays a core role in many appli-cations. One of the emerging application areas of particle systems is the analysis of molecular structures since the morphology of a molecule has been recognized as one of the most important factors ...

It has been generally accepted that the structure of molecule is one of the most important factor... more It has been generally accepted that the structure of molecule is one of the most important factors which determine the functions of a molecule. Hence, studies have been conducted to analyze the structure of a molecule. Molecular surface is an important example of molecular structure. Given a molecular surface, the area and volume of the molecule can be computed to facilitate problems such as protein docking and folding. Therefore, it is important to compute a molecular surface precisely and efficiently. This paper presents an algorithm for correctly and efficiently computing the blending surfaces of a protein which is an important part of the molecular surface. Assuming that the Voronoi diagram of atoms of a protein is given, we first compute the β-shape of the protein corresponding to a solvent probe. Then, we use a search space reduction technique for the intersection tests while the link blending surface is computed. Once a β-shape is obtained, the blending surfaces corresponding to a given solvent probe can be computed in O(n) in the worst case, where n is the number of atoms. The correctness and efficiency of the algorithm stem from the powerful properties of β-shape, quasitriangulation, and the interworld data structure.

Computer-aided Design, 2010

As the molecular shape determines the functions of a molecule, understanding molecular shapes is ... more As the molecular shape determines the functions of a molecule, understanding molecular shapes is important for understanding the biological system of life and thus for designing drugs. To properly define a molecular shape, the definition and computation of the boundary or the surface of a molecule is the most fundamental information. Assuming the hard sphere model of atoms in a

Protein-ligand docking is to predict the location and orientation of a ligand with respect to a p... more Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a

Given the atomic complex of protein, it is important to understand the interactions among protein... more Given the atomic complex of protein, it is important to understand the interactions among proteins. One of the approaches to the problem is to analyze the geometric structure of a protein because it is known that its geometric structure directly determines the protein functions. The molecular surface of the protein is one of the important geometric structure for the analysis of the protein. This paper presents an algorithm for precisely and efficiently computing the molecular surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the molecular surface is computed by employing the blending operation on the atomic complex of the protein.

Molecular shape is one of the most critical factors that determine molecular function. To properl... more Molecular shape is one of the most critical factors that determine molecular function. To properly understand the function of a molecule, it is necessary to explore its geometric properties more effectively and efficiently in addition to its physicochemical properties. Due to the complexity of the problems in biomolecular structure, in-silico approach is inevitable for many cases and is becoming more popular. In this paper, we introduce BetaMol, a comprehensive, powerful graphics-based software for molecular modeling, analysis, and visualization. BetaMol is based on the recent theory of the betacomplex which is derived from the Voronoi diagram of spheres. The entire set of powerful features of BetaMol is completely based on a single framework of the mathematically rigorous and computationally efficient theory of beta-complex. BetaMol is implemented in the standard C++ language with the OpenGL graphics library on Windows platform. Both BetaMol and some of its important functions ported for Linux platform are freely available at Voronoi Diagram Research Center website (http://voronoi.hanyang.ac.kr).

Journal of Molecular Graphics & Modelling, 2007

Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, calle... more Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes. #

Journal of Molecular Graphics & Modelling, 2007

Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, calle... more Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes. #

1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul,... more 1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, Korea dskim@email.hanyang.ac.kr {donguk, jhryu}@cadcam.hanyang.ac.kr 2 Department of Mathematical Engineering and ...

1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul,... more 1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, Korea dskim@email.hanyang.ac.kr {donguk, jhryu}@cadcam.hanyang.ac.kr 2 Department of Mathematical Engineering and ...

Computer-aided Design, 2010

The proximity and topology among particles are often the most important factor for understanding ... more The proximity and topology among particles are often the most important factor for understanding the spatial structure of particles. Reasoning the morphological structure of molecules and reconstructing a surface from a point set are examples where proximity among particles is important. Traditionally, the Voronoi diagram of points, the power diagram, the Delaunay triangulation, and the regular triangulation, etc. have been used for understanding proximity among particles. In this paper, we present the theory of the β-shape and the β-complex and the corresponding algorithms for reasoning proximity among a set of spherical particles, both using the quasi-triangulation which is the dual of the Voronoi diagram of spheres. Given the Voronoi diagram of spheres, we first transform the Voronoi diagram to the quasi-triangulation.

Computer-aided Design, 2009

Given a molecule, which consists of a set of atoms, a molecular surface is defined for a spherica... more Given a molecule, which consists of a set of atoms, a molecular surface is defined for a spherical probe approximating a solvent molecule. Molecular surface is used for both the visualization of the molecule and the computation of various molecular properties such as the area and volume of a protein, which are important for studying problems such as protein docking and folding.

Computer-aided Design, 2006

The Voronoi diagram of a point set has been extensively used in various disciplines ever since it... more The Voronoi diagram of a point set has been extensively used in various disciplines ever since it was first proposed. Its application realms have been even further extended to estimate the shape of point clouds when Edelsbrunner and Mücke introduced the concept of α-shape based on the Delaunay triangulation of a point set.

Computer-aided Design, 2007

A protein consists of linearly combined amino acids via peptide bonds, and an amino acid consists... more A protein consists of linearly combined amino acids via peptide bonds, and an amino acid consists of atoms. It is known that the geometric structure of a protein is the primary factor which determines the functions of the protein.

Abstract. Protein consists of amino acids, and an amino acid consists of atoms. Given a protein, ... more Abstract. Protein consists of amino acids, and an amino acid consists of atoms. Given a protein, understanding its functions is critical for vari-ous reasons for designing new drugs, treating diseases, and so on. Due to recent researches, it is now known that the structure of ...

Journal of Zhejiang University Science, 2006

Pockets in proteins have been known to be very important for the life process. There have been se... more Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.

ABSTRACT In recent years, there have been extensive studies on biological systems such as protein... more ABSTRACT In recent years, there have been extensive studies on biological systems such as proteins. Being one of the most important aspects, the geometry has been more important since the morphology of a molecular system is known to determine the critical functions of the molecule. In the study of the shape and the structure of a molecule, the representation of proximity information among atoms in the molecule is the most fundamental research issue. In this paper, we present a ?-shape and a ?-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known a-shape and a- complex (and their weighted counterparts as well). To compute a ?-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasitriangulation which is the topological dual of the Voronoi diagram. Then, we compute a ?-complex from the quasitriangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a ?-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a ?-shape for a particular ? consisting of k simplices can be located O(logm + k) time in the worst case from the simplicies in the ?-complex sorted according to the interval values.

Advanced Functional Materials, 2010

Journal of Biomolecular Structure & Dynamics, 2011

This paper presents an approach and a software, BetaDock, to the docking problem by putting the p... more This paper presents an approach and a software, BetaDock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the β-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the β-complex corresponding to water molecule is computed. Then, the boundary of the β-complex defines the β-shape which has the complete proximity information among all atoms on the receptor boundary. From the β-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that BetaDock is superior to a popular docking software AutoDock 4.

Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defi... more Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defined with respect to a probe approximating a solvent molecule. This paper presents an efficient, as efficient as the realtime, algorithm to triangulate the blending surfaces which is the most critical subset of a molecular surface. For the quick evaluation of points on the surface, the proposed algorithm uses masks which are similar in their concepts to those in subdivision surfaces. More fundamentally, the proposed algorithm takes advantage of the concise representation of topology among atoms stored in the β-shape which is indeed used in the computation of the blending surface itself. Given blending surfaces and the corresponding β-shape, the proposed algorithm triangulates the blending surfaces in O(c · m) time in the worst case, where m is the number of boundary atoms in the protein and c is the number of point evaluations on a patch in the blending surface.

Summary. The topology among particles frequently plays a core role in many appli-cations. One of ... more Summary. The topology among particles frequently plays a core role in many appli-cations. One of the emerging application areas of particle systems is the analysis of molecular structures since the morphology of a molecule has been recognized as one of the most important factors ...

It has been generally accepted that the structure of molecule is one of the most important factor... more It has been generally accepted that the structure of molecule is one of the most important factors which determine the functions of a molecule. Hence, studies have been conducted to analyze the structure of a molecule. Molecular surface is an important example of molecular structure. Given a molecular surface, the area and volume of the molecule can be computed to facilitate problems such as protein docking and folding. Therefore, it is important to compute a molecular surface precisely and efficiently. This paper presents an algorithm for correctly and efficiently computing the blending surfaces of a protein which is an important part of the molecular surface. Assuming that the Voronoi diagram of atoms of a protein is given, we first compute the β-shape of the protein corresponding to a solvent probe. Then, we use a search space reduction technique for the intersection tests while the link blending surface is computed. Once a β-shape is obtained, the blending surfaces corresponding to a given solvent probe can be computed in O(n) in the worst case, where n is the number of atoms. The correctness and efficiency of the algorithm stem from the powerful properties of β-shape, quasitriangulation, and the interworld data structure.

Computer-aided Design, 2010

As the molecular shape determines the functions of a molecule, understanding molecular shapes is ... more As the molecular shape determines the functions of a molecule, understanding molecular shapes is important for understanding the biological system of life and thus for designing drugs. To properly define a molecular shape, the definition and computation of the boundary or the surface of a molecule is the most fundamental information. Assuming the hard sphere model of atoms in a

Protein-ligand docking is to predict the location and orientation of a ligand with respect to a p... more Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a

Given the atomic complex of protein, it is important to understand the interactions among protein... more Given the atomic complex of protein, it is important to understand the interactions among proteins. One of the approaches to the problem is to analyze the geometric structure of a protein because it is known that its geometric structure directly determines the protein functions. The molecular surface of the protein is one of the important geometric structure for the analysis of the protein. This paper presents an algorithm for precisely and efficiently computing the molecular surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the molecular surface is computed by employing the blending operation on the atomic complex of the protein.

Molecular shape is one of the most critical factors that determine molecular function. To properl... more Molecular shape is one of the most critical factors that determine molecular function. To properly understand the function of a molecule, it is necessary to explore its geometric properties more effectively and efficiently in addition to its physicochemical properties. Due to the complexity of the problems in biomolecular structure, in-silico approach is inevitable for many cases and is becoming more popular. In this paper, we introduce BetaMol, a comprehensive, powerful graphics-based software for molecular modeling, analysis, and visualization. BetaMol is based on the recent theory of the betacomplex which is derived from the Voronoi diagram of spheres. The entire set of powerful features of BetaMol is completely based on a single framework of the mathematically rigorous and computationally efficient theory of beta-complex. BetaMol is implemented in the standard C++ language with the OpenGL graphics library on Windows platform. Both BetaMol and some of its important functions ported for Linux platform are freely available at Voronoi Diagram Research Center website (http://voronoi.hanyang.ac.kr).

Journal of Molecular Graphics & Modelling, 2007

Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, calle... more Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes. #

Journal of Molecular Graphics & Modelling, 2007

Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, calle... more Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes. #

1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul,... more 1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, Korea dskim@email.hanyang.ac.kr {donguk, jhryu}@cadcam.hanyang.ac.kr 2 Department of Mathematical Engineering and ...

1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul,... more 1 Department of Industrial Engineering, Hanyang University 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, Korea dskim@email.hanyang.ac.kr {donguk, jhryu}@cadcam.hanyang.ac.kr 2 Department of Mathematical Engineering and ...

Computer-aided Design, 2010

The proximity and topology among particles are often the most important factor for understanding ... more The proximity and topology among particles are often the most important factor for understanding the spatial structure of particles. Reasoning the morphological structure of molecules and reconstructing a surface from a point set are examples where proximity among particles is important. Traditionally, the Voronoi diagram of points, the power diagram, the Delaunay triangulation, and the regular triangulation, etc. have been used for understanding proximity among particles. In this paper, we present the theory of the β-shape and the β-complex and the corresponding algorithms for reasoning proximity among a set of spherical particles, both using the quasi-triangulation which is the dual of the Voronoi diagram of spheres. Given the Voronoi diagram of spheres, we first transform the Voronoi diagram to the quasi-triangulation.

Computer-aided Design, 2009

Given a molecule, which consists of a set of atoms, a molecular surface is defined for a spherica... more Given a molecule, which consists of a set of atoms, a molecular surface is defined for a spherical probe approximating a solvent molecule. Molecular surface is used for both the visualization of the molecule and the computation of various molecular properties such as the area and volume of a protein, which are important for studying problems such as protein docking and folding.

Computer-aided Design, 2006

The Voronoi diagram of a point set has been extensively used in various disciplines ever since it... more The Voronoi diagram of a point set has been extensively used in various disciplines ever since it was first proposed. Its application realms have been even further extended to estimate the shape of point clouds when Edelsbrunner and Mücke introduced the concept of α-shape based on the Delaunay triangulation of a point set.

Computer-aided Design, 2007

A protein consists of linearly combined amino acids via peptide bonds, and an amino acid consists... more A protein consists of linearly combined amino acids via peptide bonds, and an amino acid consists of atoms. It is known that the geometric structure of a protein is the primary factor which determines the functions of the protein.