메뉴 건너뛰기




Volumn 8110, Issue , 2013, Pages 92-111

Tunnels and voids in molecules via voronoi diagrams and beta-complexes

Author keywords

beta complex; beta shape; bounding state; external structure; molecular structure; quasi triangulation; simplexes; simplicial complex; union of disks; union of spheres; van der Waals region; Voronoi diagram of spheres

Indexed keywords

COMPUTATIONAL GEOMETRY; MOLECULAR STRUCTURE; MOLECULES; VAN DER WAALS FORCES;

EID: 84892778855     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-41905-8_7     Document Type: Conference Paper
Times cited : (12)

References (41)
  • 1
    • 84892694991 scopus 로고    scopus 로고
    • Voronoi Diagram Research Center (2011)
    • Voronoi Diagram Research Center (2011), http://voronoi. hanyang. ac. kr/
  • 3
    • 33646143990 scopus 로고    scopus 로고
    • Recognition of docking sites on a protein using ?-shape based on Voronoi diagram of atoms
    • Kim, D. S. Cho, C. H. Kim, D.Cho, Y.: Recognition of docking sites on a protein using ?-shape based on Voronoi diagram of atoms. Computer-Aided Design 38(5), 431-443 (2006)
    • (2006) Computer-Aided Design , vol.38 , Issue.5 , pp. 431-443
    • Kim, D.S.1    Cho, C.H.2    Kim, D.3    Cho, Y.4
  • 6
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt, G. J. Jones, T. A.: Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallographica Section D 50, 178-185 (1994)
    • (1994) Acta Crystallographica Section D , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 7
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski, R. A.: SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics 13, 323-330 (1995)
    • (1995) Journal of Molecular Graphics , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 12
    • 33847076903 scopus 로고    scopus 로고
    • Identification of tunnels in proteins, nucleic acids inorganic materials and molecular ensembles
    • Damborsky, J. Petrek, M.Banas, P.Otyepka, M.: Identification of tunnels in proteins, nucleic acids inorganic materials and molecular ensembles. Biotechnology Journal 2, 62-67 (2007)
    • (2007) Biotechnology Journal , vol.2 , pp. 62-67
    • Damborsky, J.1    Petrek, M.2    Banas, P.3    Otyepka, M.4
  • 13
    • 35748972048 scopus 로고    scopus 로고
    • MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
    • Petrek, M.Kosinova, P.Koca, J.Otyepka, M.: MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 15(11), 1357-1363 (2007)
    • (2007) Structure , vol.15 , Issue.11 , pp. 1357-1363
    • Petrek, M.1    Kosinova, P.2    Koca, J.3    Otyepka, M.4
  • 14
    • 84861407812 scopus 로고    scopus 로고
    • Computation of tunnels in protein molecules using Delaunay triangulation
    • Medek, P.Benes, P.Sochor, J.: Computation of tunnels in protein molecules using Delaunay triangulation. Journal of WSCG 15, 107-114 (2007)
    • (2007) Journal of WSCG , vol.15 , pp. 107-114
    • Medek, P.1    Benes, P.2    Sochor, J.3
  • 15
    • 42149108442 scopus 로고    scopus 로고
    • Visualization of tunnels in protein molecules
    • Kozl?lova, B. Andres, F.Sochor, J.: Visualization of tunnels in protein molecules. In: AfriGraph 2007, pp. 111-209 (2007)
    • (2007) AfriGraph 2007 , pp. 111-209
    • Kozllova Andres, B.F.1    Sochor, J.2
  • 18
    • 77955773185 scopus 로고    scopus 로고
    • Approximating the pathway axis and the persistence diagrams for a collection of balls in 3-space
    • Yaffe, E.Halperin, D.: Approximating the pathway axis and the persistence diagrams for a collection of balls in 3-space. Discrete &Computational Geometry 44, 660-685 (2010)
    • (2010) Discrete &Computational Geometry , vol.44 , pp. 660-685
    • Yaffe, E.1    Halperin, D.2
  • 19
    • 57649229060 scopus 로고    scopus 로고
    • HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures
    • Ho, B. K. Gruswitz, F.: HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures. BMC Structural Biology 8(1), 49 (2008)
    • (2008) BMC Structural Biology , vol.8 , Issue.1 , pp. 49
    • Ho, B.K.1    Gruswitz, F.2
  • 20
    • 58849142521 scopus 로고    scopus 로고
    • Finding and characterizing tunnels in macromolecules with application to ion channels and pores
    • Coleman, R. G. Sharp, K. A.: Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophysical Journal 96, 632-645 (2009)
    • (2009) Biophysical Journal , vol.96 , pp. 632-645
    • Coleman, R.G.1    Sharp, K.A.2
  • 22
    • 35048863957 scopus 로고    scopus 로고
    • Implementation of the voronoi-delaunay method for analysis of intermolecular voids
    • In: Lagana, A. Gavrilova, M. L. Kumar, V.Mun, Y.Tan, C. J. K. Gervasi, O. (eds.) Springer, Heidelberg
    • Anikeenko, A. V. Alinchenko, M. G. Voloshin, V. P. Medvedev, N. N. Gavrilova, M. L. Jedlovszky, P.: Implementation of the voronoi-delaunay method for analysis of intermolecular voids. In: Lagana, A. Gavrilova, M. L. Kumar, V.Mun, Y.Tan, C. J. K. Gervasi, O. (eds.) ICCSA 2004. LNCS, vol. 3045, pp. 217-226. Springer, Heidelberg (2004)
    • (2004) ICCSA 2004. LNCS , vol.3045 , pp. 217-226
    • Anikeenko, A.V.1    Alinchenko, M.G.2    Voloshin, V.P.3    Medvedev, N.N.4    Gavrilova, M.L.5    Jedlovszky, P.6
  • 23
    • 84962376833 scopus 로고    scopus 로고
    • Free energy of solvation from molecular dynamics simulation applying voronoi-delaunay triangulation to the cavity creation
    • Goncalves, P. F. B. Stassen, H.: Free energy of solvation from molecular dynamics simulation applying voronoi-delaunay triangulation to the cavity creation. Journal of Chemical Physics 123(21), 214109 (2005)
    • (2005) Journal of Chemical Physics , vol.123 , Issue.21 , pp. 214109
    • Goncalves, P.F.B.1    Stassen, H.2
  • 24
    • 22944434527 scopus 로고    scopus 로고
    • Euclidean Voronoi diagram of 3D balls and its computation via tracing edges
    • Kim, D. S. Cho, Y.Kim, D.: Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Computer-Aided Design 37(13), 1412-1424 (2005)
    • (2005) Computer-Aided Design , vol.37 , Issue.13 , pp. 1412-1424
    • Kim, D.S.1    Cho, Y.2    Kim, D.3
  • 26
    • 84867663377 scopus 로고    scopus 로고
    • Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules
    • Kim, D. S. Cho, Y.Ryu, J.Kim, J. K. Kim, D.: Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules. Computer-Aided Design 45(1), 35-52 (2013)
    • (2013) Computer-Aided Design , vol.45 , Issue.1 , pp. 35-52
    • Kim, D.S.1    Cho, Y.2    Ryu, J.3    Kim, J.K.4    Kim, D.5
  • 27
    • 77955565392 scopus 로고    scopus 로고
    • Quasi-worlds and quasi-operators on quasitriangulations
    • Kim, D. S. Cho, Y.Sugihara, K.: Quasi-worlds and quasi-operators on quasitriangulations. Computer-Aided Design 42(10), 874-888 (2010)
    • (2010) Computer-Aided Design , vol.42 , Issue.10 , pp. 874-888
    • Kim, D.S.1    Cho, Y.2    Sugihara, K.3
  • 28
    • 33745813533 scopus 로고    scopus 로고
    • Quasi-triangulation and interworld data structure in three dimensions
    • Kim, D. S. Kim, D.Cho, Y.Sugihara, K.: Quasi-triangulation and interworld data structure in three dimensions. Computer-Aided Design 38(7), 808-819 (2006)
    • (2006) Computer-Aided Design , vol.38 , Issue.7 , pp. 808-819
    • Kim, D.S.1    Kim, D.2    Cho, Y.3    Sugihara, K.4
  • 29
  • 30
    • 77955569416 scopus 로고    scopus 로고
    • Three-dimensional beta-shapes and beta-complexes via quasi-triangulation
    • Kim, D. S. Cho, Y.Sugihara, K.Ryu, J.Kim, D.: Three-dimensional beta-shapes and beta-complexes via quasi-triangulation. Computer-Aided Design 42(10), 911-929 (2010)
    • (2010) Computer-Aided Design , vol.42 , Issue.10 , pp. 911-929
    • Kim, D.S.1    Cho, Y.2    Sugihara, K.3    Ryu, J.4    Kim, D.5
  • 31
    • 67349280969 scopus 로고    scopus 로고
    • Triangulation of molecular surfaces
    • Ryu, J.Cho, Y.Kim, D. S.: Triangulation of molecular surfaces. Computer-Aided Design 41(6), 463-478 (2009)
    • (2009) Computer-Aided Design , vol.41 , Issue.6 , pp. 463-478
    • Ryu, J.1    Cho, Y.2    Kim, D.S.3
  • 32
    • 36448970902 scopus 로고    scopus 로고
    • Molecular surfaces on proteins via beta shapes
    • Ryu, J.Park, R.Kim, D. S.: Molecular surfaces on proteins via beta shapes. Computer-Aided Design 39(12), 1042-1057 (2007)
    • (2007) Computer-Aided Design , vol.39 , Issue.12 , pp. 1042-1057
    • Ryu, J.1    Park, R.2    Kim, D.S.3
  • 33
    • 78649830867 scopus 로고    scopus 로고
    • Proteinligand docking based on beta-shape
    • In: Gavrilova, M. L. Tan, C. J. K. Anton, F. (eds.) Springer, Heidelberg
    • Kim, C.-M. Won, C.-I. Kim, J.-K. Ryu, J.Bhak, J.Kim, D.-S.: Proteinligand docking based on beta-shape. In: Gavrilova, M. L. Tan, C. J. K. Anton, F. (eds.) Transactions on Computational Science IX. LNCS, vol. 6290, pp. 123-138. Springer, Heidelberg (2010)
    • (2010) Transactions on Computational Science IX. LNCS , vol.6290 , pp. 123-138
    • Kim, C.-M.1    Won, C.-I.2    Kim, J.-K.3    Ryu, J.4    Bhak, J.5    Kim, D.-S.6
  • 35
    • 84892737367 scopus 로고    scopus 로고
    • Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets
    • Kim, D. S. Ryu, J.Shin, H.Cho, Y.: Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets. Journal of Computational Chemistry 12(3), 1225-1283 (2012)
    • (2012) Journal of Computational Chemistry , vol.12 , Issue.3 , pp. 1225-1283
    • Kim, D.S.1    Ryu, J.2    Shin, H.3    Cho, Y.4
  • 38
    • 20544433165 scopus 로고
    • Van der Waals volumes and radii
    • Bondi, A.: van der Waals volumes and radii. Journal of Physical Chemistry 68, 441-451 (1964)
    • (1964) Journal of Physical Chemistry , vol.68 , pp. 441-451
    • Bondi, A.1
  • 41
    • 84892718577 scopus 로고    scopus 로고
    • RCSB Protein Data Bank (2009)
    • RCSB Protein Data Bank (2009), http://www. rcsb. org/pdb/


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.