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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>
BetaCavityWeb: a webserver for molecular voids and channels
Kim, Jae-Kwan,Cho, Youngsong,Lee, Mokwon,Laskowski, Roman A.,Ryu, Seong Eon,Sugihara, Kokichi,Kim, Deok-Soo Oxford University Press 2015 Nucleic acids research Vol.43 No.w1
<P>Molecular cavities, which include voids and channels, are critical for molecular function. We present a webserver, <I>BetaCavityWeb</I>, which computes these cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex. The correctness of the computed result and computational efficiency are both mathematically guaranteed. BetaCavityWeb is freely accessible at the Voronoi Diagram Research Center (VDRC) (http://voronoi.hanyang.ac.kr/betacavityweb).</P>
MGOS: A library for molecular geometry and its operating system
Kim, Deok-Soo,Ryu, Joonghyun,Cho, Youngsong,Lee, Mokwon,Cha, Jehyun,Song, Chanyoung,Kim, Sang Wha,Laskowski, Roman A.,Sugihara, Kokichi,Bhak, Jong,Ryu, Seong Eon Elsevier 2020 Computer physics communications Vol.251 No.-
<P><B>Abstract</B></P> <P>The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present “Molecular Geometry (MG)” as a theoretical framework accompanied by “MG Operating System (MGOS)” which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering.</P> <P><B>Program summary</B></P> <P> <I>Program Title:</I> Molecular Geometry Operating System (MGOS)</P> <P> <I>Program Files doi:</I> http://dx.doi.org/10.17632/hp2wmvxsfz.1 </P> <P> <I>Licensing provisions:</I> CC By 4.0</P> <P> <I>Programming language:</I> C++</P> <P> <I>Supplementary material:</I> (1) Supplementary Video 1, (2) Supplementary Video 2, (3) Supplementary Video 3, (4) Supplementary Video 4, (5) MGOS manual, and (6) 300 test PDB structure files</P> <P> <I>Nature of problem:</I> For both organic and inorganic molecules, structure determines molecular function and molecular structure is highly correlated with molecular shape or geometry. Hence, many studies were conducted for the analysis and evaluation of the geometry of atomic arrangement. However, most studies were based on Monte Carlo, grid-counting, or approximation methods and a high-quality solution requires heavy computational resources, not to mention its dependency on computation environment. In this paper, we introduce a unified framework of computational library, Molecular Geometry Operating System (MGOS), based on an analytic method for the molecular geometry of atomic arrangements. We believe that the powerful MGOS application programming interface (API) functions will free scientists from developing and implementing complicated geometric algorithms and let them focus on more important scientific problems.</P> <P> <I>Solution method:</I> Molecular Geometry (MG) is a general framework of mathematical/computational methods for solving molecular structure problems using a geometry-priority philosophy and is implemented by MGOS which is a library of callable C++ API functions. MGOS is developed based on the Voronoi diagram of three-dimensional spheres and its two derivative constructs called the quasi-triangulation and beta-complex. Note that this Voronoi diagram is different from the ordinary Voronoi diagram of points where the points are atom centers. Being an analytic method, the solutions of many geometric queries on atomic arrangement, if not all, are obtained correctly and quickly. The MGOS architecture is carefully designed in a three-tier architecture so that future modifications and/or improvements can be reflected in the application programs with no additional programming by users.</P>