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Molecular surfaces of proteins based on β-shapes and Voronoi diagrams of atoms
Joonghyun Ryu,Rhohun Park,Choel-Hyung Cho,Deok-Soo Kim 한국산업응용수학회 2005 한국산업응용수학회 학술대회 논문집 Vol.- No.-
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 ß-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 ß-shape with an appropriate probe. Then, the molecular surface is computed by employing the blending operation on the atomic complex of 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) 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.
Ryu, JoongHyun,Cho, Dongsoo,Cho, Youngsong,Kim, Deok-Soo 한국경영과학회 1999 한국경영과학회 학술대회논문집 Vol.- No.1
Intersection problem occurs in various engineering application areas, such as CAD/CAM, GIS, computer graphics, etc. Most of all, intersection algorithms are fundamental to CAD/CAM. Parametric curves have been frequently used in CAGD and thus intersection algorithm between parametric curves been studied intensively in several respects such as the speed, the robustness and the efficiency. Although many intersection algorithms have been published, there exists no algorithm that is satisfactory in all the above three aspects. The intersection techniques that appear in the literature can be classified into three categories; Newton-Raphson iteration method, subdivision method and implicitization method. Newton-Raphson iteration-wise method shows a good convergence rate in case that a good initial seed is given. Otherwise, it provides a wrong solution or diverges. Bezier clipping algorithm copes with intersection problem like an intelligent Newton method. Though it is faster than Implicitization algorithm and Interval subdivision for curve of degree less than 5. Intersection algorithm based on subdivision method divides the original intersection problem into easier ones and then conquers the each divided problem. Be´zier subdivision and interval subdivision algorithm is included in this category. Implicitization method transforms intersection problem to the problem of finding a single polynomial root by substitution a parametric from curve into the implicitized curves. This approach is known to be fastest in computing the intersections between curves of degrees less than quintics. In this paper, an algorithm for intersecting Bezier curves is provided and is extended to an algorithm for intersections between NURBS curves. The algorithm characterized both curves to be intersected and approximates them in lower degree curves. Implicitization technique is applied to the intersections between approximated low degree curves for locating initial solution. Then a good initial solution is obtained and Newton-Raphson iteration converge to a true intersection quickly abs robustly. Tangential case overlapping case are not considered in the pro^+posed algorithm.
Ryu, Joonghyun,Lee, Mokwon,Cha, Jehyun,Laskowski, Roman A.,Ryu, Seong Eon,Kim, Deok-Soo Oxford University Press 2016 Nucleic acids research Vol.44 No.w1
<P>Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement.</P>
Joonghyun Ryu,Rhohun Park,Deok-Soo Kim 한국산업경영시스템학회 2005 한국산업경영시스템학회 학술대회 Vol.2005 No.춘계
Given a protein, it is often necessary to study its geometric and physicochemical properties for studying its structure and predicting funtions of a protein. In this case, a connolly surface of a protein plays important roles for these purpose. A protein consists of a set of amino acids and a set of atoms comprise an amino acide. Since an atom can be represented by a hard 3D sphere in van der Waals model, a protein is usually modeled as a set of 3D spheres. In this paper, we present the algorithm for computing a connolly surface using Euclidean Voronoi diagram atoms of a protein. The algorithm initially locates the exterior aotms of a protein where connolly surface patches exist and computes the patches by tracking their boundary curves. Since a Euclidean Voronoi diagram is uniquely defined independent of probe radius different from other geometric structures, the connolly surfaces defined by probes of different radii can be computed without re-computing the Euclidean Voronoi diagram.