MGOS: A library for molecular geometry and its operating system.

Youngsong Cho

Deok-Soo Kim Joonghyun Ryu Youngsong Cho Mokwon Lee Jehyun Cha Chanyoung Song Sangwha Kim Roman A. Laskowski Kokichi Sugihara Jong Bhak Seong Eon Ryu MGOS: A library for molecular geometry and its operating system. 107101 2020 251 Comput. Phys. Commun. https://doi.org/10.1016/j.cpc.2019.107101 https://www.wikidata.org/entity/Q126578959 db/journals/cphysics/cphysics251.html#KimRCLCSKLSBR20

Donguk Kim 0001 Mokwon Lee Youngsong Cho Deok-Soo Kim Beta-complex versus Alpha-complex: Similarities and Dissimilarities. 1686-1701 2020 26 IEEE Trans. Vis. Comput. Graph. 4 https://doi.org/10.1109/TVCG.2018.2873633 https://www.wikidata.org/entity/Q58596963 db/journals/tvcg/tvcg26.html#KimLCK20

Deok-Soo Kim Joonghyun Ryu Youngsong Cho Mokwon Lee Jehyun Cha Chanyoung Song Sangwha Kim Roman A. Laskowski Kokichi Sugihara Jong Bhak Seong Eon Ryu MGOS: A Library for Molecular Geometry and its Operating System. 2019 abs/1906.12141 CoRR http://arxiv.org/abs/1906.12141 db/journals/corr/corr1906.html#abs-1906-12141

Mokwon Lee Qing Fang Youngsong Cho Joonghyun Ryu Ligang Liu 0001 Deok-Soo Kim Support-free hollowing for 3D printing via Voronoi diagram of ellipses. 23-36 2018 101 Comput. Aided Des. https://doi.org/10.1016/j.cad.2018.03.007 https://www.wikidata.org/entity/Q129981123 db/journals/cad/cad101.html#LeeFCRLK18

Jae-Kwan Kim 0001 Youngsong Cho Mokwon Lee Roman A. Laskowski Seong Eon Ryu Kokichi Sugihara Deok-Soo Kim BetaCavityWeb: a webserver for molecular voids and channels. W413-W418 2015 43 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkv360 https://www.wikidata.org/entity/Q41489602 db/journals/nar/nar43.html#KimCLLRSK15

Jae-Kwan Kim 0001 Youngsong Cho Donguk Kim 0001 Deok-Soo Kim Voronoi diagrams, quasi-triangulations, and beta-complexes for disks in R<sup>2</sup>: the theory and implementation in BetaConcept. 79-87 2014 1 J. Comput. Des. Eng. 2 https://doi.org/10.7315/JCDE.2014.008 db/journals/jcde/jcde1.html#KimCKK14

Youngsong Cho Jae-Kwan Kim 0001 Joonghyun Ryu Mokwon Lee Jehyun Cha Chanyoung Song Deok-Soo Kim Molecular Geometry and BULL! 261-268 2014 CW https://doi.org/10.1109/CW.2014.43 https://doi.ieeecomputersociety.org/10.1109/CW.2014.43 conf/cw/2014 db/conf/cw/cw2014.html#ChoKRLCSK14 Jae-Kwan Kim 0001 Youngsong Cho Mokwon Lee Jehyun Cha Chanyoung Song Deok-Soo Kim Donguk Kim 0001 BetaConcept: A Program for Voronoi Diagrams, Dual Structures, and Complexes in the Plane. 233-236 2014 ICCSA (Workshops/Short Papers/Posters) https://doi.org/10.1109/ICCSA.2014.53 https://doi.ieeecomputersociety.org/10.1109/ICCSA.2014.53 conf/iccsa/2014-w db/conf/iccsa/iccsa2014-w.html#KimCLCSKK14 Donguk Kim 0001 Youngsong Cho Jae-Kwan Kim 0001 Yuan-Shin Lee Deok-Soo Kim How Similar Are Quasi-, Regular, and Delaunay Triangulations in ℝ3? 381-393 2014 ICCSA (2) https://doi.org/10.1007/978-3-319-09129-7_29 conf/iccsa/2014-2 db/conf/iccsa/iccsa2014-2.html#KimCKLK14 Deok-Soo Kim Youngsong Cho Jae-Kwan Kim 0001 Joonghyun Ryu Mokwon Lee Jehyun Cha Chanyoung Song BULL! - The Molecular Geometry Engine Based on Voronoi Diagram, Quasi-Triangulation, and Beta-Complex. 206-213 2014 ICMS https://doi.org/10.1007/978-3-662-44199-2_33 conf/icms/2014 db/conf/icms/icms2014.html#KimCKRLCS14

Deok-Soo Kim Youngsong Cho Joonghyun Ryu Jae-Kwan Kim 0001 Donguk Kim 0001 Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules. 35-52 2013 45 Comput. Aided Des. 1 https://doi.org/10.1016/j.cad.2012.03.005 db/journals/cad/cad45.html#KimCRKK13

Deok-Soo Kim Youngsong Cho Jae-Kwan Kim 0001 Kokichi Sugihara Tunnels and Voids in Molecules via Voronoi Diagrams and Beta-Complexes. 92-111 2013 20 Trans. Comput. Sci. https://doi.org/10.1007/978-3-642-41905-8_7 journals/tcos/2013-20 db/journals/tcos/tcos20.html#KimCKS13

Donguk Kim 0001 Youngsong Cho Deok-Soo Kim Anomaly Occurrences in Quasi-triangulations and Beta-complexes. 82-88 2013 ISVD https://doi.org/10.1109/ISVD.2013.18 https://doi.ieeecomputersociety.org/10.1109/ISVD.2013.18 conf/isvd/2013 db/conf/isvd/isvd2013.html#KimCK13

Deok-Soo Kim Jae-Kwan Kim 0001 Youngsong Cho Chong-Min Kim Querying simplexes in quasi-triangulation. 85-98 2012 44 Comput. Aided Des. 2 https://doi.org/10.1016/j.cad.2011.09.010 db/journals/cad/cad44.html#KimKCK12

Deok-Soo Kim Youngsong Cho Jae-Kwan Kim 0001 Joonghyun Ryu QTF: Quasi-triangulation file format. 835-845 2012 44 Comput. Aided Des. 9 https://doi.org/10.1016/j.cad.2012.04.003 db/journals/cad/cad44.html#KimCKR12

Deok-Soo Kim Joonghyun Ryu Hayong Shin Youngsong Cho Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets. 1252-1273 2012 33 J. Comput. Chem. 13 https://doi.org/10.1002/jcc.22956 https://www.wikidata.org/entity/Q51407982 db/journals/jcc/jcc33.html#KimRSC12

Youngsong Cho Jae-Kwan Kim 0001 Chung In Won Joonghyun Ryu Chong-Min Kim Deok-Soo Kim BetaMol: Molecular Modeling, Analysis, and Visualization Software Based on the Beta-Complex Derived from the Voronoi Diagram. 48-57 2011 ISVD https://doi.org/10.1109/ISVD.2011.15 https://doi.ieeecomputersociety.org/10.1109/ISVD.2011.15 conf/isvd/2011 db/conf/isvd/isvd2011.html#ChoKWRKK11

Deok-Soo Kim Changhee Lee Youngsong Cho Donguk Kim 0001 Manifoldization of beta-shapes in O(n) time. 322-339 2010 42 Comput. Aided Des. 4 https://doi.org/10.1016/j.cad.2009.12.005 db/journals/cad/cad42.html#KimLCK10

Deok-Soo Kim Youngsong Cho Joonghyun Ryu Chong-Min Kim Topologies of surfaces on molecules and their computation in O(n) time. 795-807 2010 42 Comput. Aided Des. 9 https://doi.org/10.1016/j.cad.2010.04.008 db/journals/cad/cad42.html#KimCRK10

Deok-Soo Kim Youngsong Cho Kokichi Sugihara Quasi-worlds and quasi-operators on quasi-triangulations. 874-888 2010 42 Comput. Aided Des. 10 https://doi.org/10.1016/j.cad.2010.06.002 db/journals/cad/cad42.html#KimCS10

Deok-Soo Kim Youngsong Cho Kokichi Sugihara Joonghyun Ryu Donguk Kim 0001 Three-dimensional beta-shapes and beta-complexes via quasi-triangulation. 911-929 2010 42 Comput. Aided Des. 10 https://doi.org/10.1016/j.cad.2010.06.004 db/journals/cad/cad42.html#KimCSRK10

Joonghyun Ryu Youngsong Cho Deok-Soo Kim Triangulation of molecular surfaces. 463-478 2009 41 Comput. Aided Des. 6 https://doi.org/10.1016/j.cad.2009.02.011 db/journals/cad/cad41.html#RyuCK09

Donguk Kim 0001 Changhee Lee Youngsong Cho Deok-Soo Kim Manifoldization of pi-Shapes by Topology Operators. 505-511 2008 GMP https://doi.org/10.1007/978-3-540-79246-8_40 conf/gmp/2008 db/conf/gmp/gmp2008.html#KimLCK08 Deok-Soo Kim Jeongyeon Seo Donguk Kim 0001 Youngsong Cho Joonghyun Ryu The beta-Shape and beta-Complex for Analysis of Molecular Structures. 47-66 2008 Generalized Voronoi Diagram https://doi.org/10.1007/978-3-540-85126-4_3 series/sci/2008-158 db/series/sci/sci158.html#KimSKCR08

Cheol-Hyung Cho Deok-Soo Kim Youngsong Cho Joonghyun Ryu Upper and lower bounds of op-code probabilities for Edgebreaker. 23-28 2007 3 Int. J. Comput. Sci. Eng. 1 https://doi.org/10.1504/IJCSE.2007.014462 db/journals/ijcse/ijcse3.html#ChoKCR07

Deok-Soo Kim Bohyung Lee Chung In Won Donguk Kim 0001 Joonghyun Ryu Youngsong Cho Chong-Min Kim Sunghoon Lee Jonghwa Bhak Multi-Resolution Protein Model. 639-652 2007 conf/iccsa/2007-2 ICCSA (2) https://doi.org/10.1007/978-3-540-74477-1_59 db/conf/iccsa/iccsa2007-2.html#KimLWKRCKLB07 Joonghyun Ryu Rhohun Park Youngsong Cho Jeongyeon Seo Deok-Soo Kim beta-shape Based Computation of Blending Surfaces on a Molecule. 189-198 2007 conf/isvd/2007 ISVD https://doi.org/10.1109/ISVD.2007.1 https://doi.ieeecomputersociety.org/10.1109/ISVD.2007.1 db/conf/isvd/isvd2007.html#RyuPCSK07 Jeongyeon Seo Youngsong Cho Donguk Kim 0001 Deok-Soo Kim An efficient algorithm for three-dimensional beta-complex and beta-shape via a quasi-triangulation. 323-328 2007 conf/sma/2007 Symposium on Solid and Physical Modeling https://doi.org/10.1145/1236246.1236292 db/conf/sma/spm2007.html#SeoCKK07

Deok-Soo Kim Cheol-Hyung Cho Donguk Kim 0001 Youngsong Cho Recognition of docking sites on a protein using <i>beta</i>-shape based on Voronoi diagram of atoms. 431-443 2006 38 Comput. Aided Des. 5 https://doi.org/10.1016/j.cad.2005.11.008 db/journals/cad/cad38.html#KimCKC06

Deok-Soo Kim Donguk Kim 0001 Youngsong Cho Kokichi Sugihara Quasi-triangulation and interworld data structure in three dimensions. 808-819 2006 38 Comput. Aided Des. 7 https://doi.org/10.1016/j.cad.2006.04.008 db/journals/cad/cad38.html#KimKCS06

Chong-Min Kim Chung In Won Youngsong Cho Donguk Kim 0001 Sunghoon Lee Jonghwa Bhak Deok-Soo Kim Interaction interfaces in proteins via the Voronoi diagram of atoms. 1192-1204 2006 38 Comput. Aided Des. 11 https://doi.org/10.1016/j.cad.2006.07.007 db/journals/cad/cad38.html#KimWCKLBK06

Youngsong Cho Donguk Kim 0001 Hyun-Chan Lee Joon Young Park Deok-Soo Kim Reduction of the Search Space in the Edge-Tracing Algorithm for the Voronoi Diagram of 3D Balls. 111-120 2006 conf/iccsa/2006-1 ICCSA (1) https://doi.org/10.1007/11751540_13 db/conf/iccsa/iccsa2006-1.html#ChoKLPK06 Jeongyeon Seo Youngsong Cho Cheol-Hyung Cho Donguk Kim 0001 Joonghyun Ryu Deok-Soo Kim The B-shape and B-complex for three-dimensional spheres. 138-147 2006 ISVD https://doi.org/10.1109/ISVD.2006.35 https://doi.ieeecomputersociety.org/10.1109/ISVD.2006.35 conf/isvd/2006 db/conf/isvd/isvd2006.html#SeoCCKRK06

Deok-Soo Kim Youngsong Cho Donguk Kim 0001 Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. 1412-1424 2005 37 Comput. Aided Des. 13 https://doi.org/10.1016/j.cad.2005.02.013 db/journals/cad/cad37.html#KimCK05

Deok-Soo Kim Cheol-Hyung Cho Youngsong Cho Chung In Won Donguk Kim 0001 Pocket Recognition on a Protein Using Euclidean Voronoi Diagram of Atoms. 707-715 2005 conf/iccsa/2005-1 ICCSA (1) https://doi.org/10.1007/11424758_73 db/conf/iccsa/iccsa2005-1.html#KimCCWK05 Donguk Kim 0001 Youngsong Cho Deok-Soo Kim Region Expansion by Flipping Edges for Euclidean Voronoi Diagrams of 3D Spheres Based on a Radial Data Structure. 716-725 2005 conf/iccsa/2005-1 ICCSA (1) https://doi.org/10.1007/11424758_74 db/conf/iccsa/iccsa2005-1.html#KimCK05 Deok-Soo Kim Donguk Kim 0001 Youngsong Cho Joonghyun Ryu Cheol-Hyung Cho Joon Young Park Hyun-Chan Lee Visualization and Analysis of Protein Structures Using Euclidean Voronoi Diagram of Atoms. 993-1002 2005 conf/iccsa/2005-3 ICCSA (3) https://doi.org/10.1007/11424857_107 db/conf/iccsa/iccsa2005-3.html#KimKCRCPL05 Deok-Soo Kim Donguk Kim 0001 Youngsong Cho Euclidean Voronoi Diagrams of 3D Spheres: Their Construction and Related Problems from Biochemistry. 255-271 2005 conf/ima-ms/2005 IMA Conference on the Mathematics of Surfaces https://doi.org/10.1007/11537908_16 db/conf/ima-ms/ima-ms2005.html#KimKC05

Deok-Soo Kim Youngsong Cho Hyun Kim Normal vector compression of 3D mesh model based on clustering and relative indexing. 1241-1250 2004 20 Future Gener. Comput. Syst. 8 https://doi.org/10.1016/j.future.2004.05.029 db/journals/fgcs/fgcs20.html#KimCK04

Deok-Soo Kim Youngsong Cho Donguk Kim 0001 Edge-tracing algorithm for euclidean voronoi diagram of 3d spheres. 176-179 2004 conf/cccg/2004 CCCG http://www.cccg.ca/proceedings/2004/28.pdf db/conf/cccg/cccg2004.html#KimCK04 Deok-Soo Kim Kwangseok Yu Youngsong Cho Donguk Kim 0001 Chee-Keng Yap Shortest Paths for Disc Obstacles. 62-70 https://doi.org/10.1007/978-3-540-24767-8_7 2004 conf/iccsa/2004-3 ICCSA (3) db/conf/iccsa/iccsa2004-3.html#KimYCKY04 Deok-Soo Kim Cheol-Hyung Cho Youngsong Cho Chang Wook Kang Hyun-Chan Lee Joon Young Park Probability Distribution of Op-Codes in Edgebreaker. 554-563 https://doi.org/10.1007/978-3-540-24709-8_59 2004 conf/iccsa/2004-2 ICCSA (2) db/conf/iccsa/iccsa2004-2.html#KimCCKLP04 Deok-Soo Kim Youngsong Cho Donguk Kim 0001 Hyun Kim Probability Distribution of Index Distances in Normal Index Array for Normal Vector Compression. 887-896 2003 conf/iccS/2003-1 International Conference on Computational Science https://doi.org/10.1007/3-540-44860-8_92 db/conf/iccS/iccS2003-1.html#KimCKK03 Youngsong Cho Deok-Soo Kim Hyun Kim Hyun-Chan Lee Joon Young Park Distribution of Vertex Indices in Edgebreaker. 448-457 https://doi.org/10.1007/3-540-44842-X_46 2003 conf/iccsa/2003-3 ICCSA (3) db/conf/iccsa/iccsa2003-3.html#ChoKKLP03 Joonghyun Ryu Youngsong Cho Deok-Soo Kim Transformation of a Dynamic B-Spline Curve into Piecewise Power Basis Representation. 82-91 2002 conf/iccS/2002-2 International Conference on Computational Science (2) https://doi.org/10.1007/3-540-46080-2_9 db/conf/iccS/iccS2002-2.html#RyuCK02 Deok-Soo Kim Youngsong Cho Donguk Kim 0001 The Compression of the Normal Vectors of 3D Mesh Models Using Clustering. 275-284 2002 conf/iccS/2002-2 International Conference on Computational Science (2) https://doi.org/10.1007/3-540-46080-2_29 db/conf/iccS/iccS2002-2.html#KimCK02 Deok-Soo Kim Youngsong Cho Hyun Kim Normal Compression Based on Clustering and Relative Indexing. 446-447 2002 conf/pg/2002 PG https://doi.org/10.1109/PCCGA.2002.1167895 https://doi.ieeecomputersociety.org/10.1109/PCCGA.2002.1167895 db/conf/pg/pg2002.html#KimCK02 Deok-Soo Kim Jaeyeol Chung Youngsong Cho Taeboom Jang Hyun Kim Geometry Compression Based on Mantissa Chunking of Vertices. 606-611 2001 conf/iv/2001 IV https://doi.org/10.1109/IV.2001.942118 https://doi.ieeecomputersociety.org/10.1109/IV.2001.942118 db/conf/iv/iv2001.html#KimCCJK01 Jong Bhak Jonghwa Bhak Jehyun Cha Cheol-Hyung Cho Jaeyeol Chung Qing Fang Taeboom Jang Chang Wook Kang Chong-Min Kim Deok-Soo Kim Donguk Kim 0001 Hyun Kim Jae-Kwan Kim 0001 Sangwha Kim Roman A. Laskowski Bohyung Lee Changhee Lee Hyun-Chan Lee Mokwon Lee Sunghoon Lee Yuan-Shin Lee Ligang Liu 0001 Joon Young Park Rhohun Park Joonghyun Ryu Seong Eon Ryu Jeongyeon Seo Hayong Shin Chanyoung Song Kokichi Sugihara Chung In Won Chee-Keng Yap Kwangseok Yu