-
1
-
-
40649097302
-
Pocket extraction on proteins via the Voronoi diagram of spheres
-
D. Kim, C.-H. Cho, Y. Cho, J. Ryu, J. Bhak, and D.-S. Kim, "Pocket extraction on proteins via the Voronoi diagram of spheres," Journal of Molecular Graphics & Modelling, vol. 26, no. 7, pp. 1104-1112, 2008.
-
(2008)
Journal of Molecular Graphics & Modelling
, vol.26
, Issue.7
, pp. 1104-1112
-
-
Kim, D.1
Cho, C.-H.2
Cho, Y.3
Ryu, J.4
Bhak, J.5
Kim, D.-S.6
-
2
-
-
33646143990
-
Recognition of docking sites on a protein using β-shape based on Voronoi diagram of atoms
-
D.-S. Kim, C.-H. Cho, D. Kim, and Y. Cho, "Recognition of docking sites on a protein using β-shape based on Voronoi diagram of atoms," Computer-Aided Design, vol. 38, no. 5, pp. 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
-
3
-
-
79959405663
-
BetaDock: Shape-priority docking method based on Beta-complex
-
D.-S. Kim, C.-M. Kim, C.-I. Won, J.-K. Kim, J. Ryu, Y. Cho, C. Lee, and J. Bhak, "BetaDock: Shape-priority docking method based on Beta-complex," Journal of Biomolecular Structure & Dynamics, vol. 29, no. 1, pp. 219-242, 2011.
-
(2011)
Journal of Biomolecular Structure & Dynamics
, vol.29
, Issue.1
, pp. 219-242
-
-
Kim, D.-S.1
Kim, C.-M.2
Won, C.-I.3
Kim, J.-K.4
Ryu, J.5
Cho, Y.6
Lee, C.7
Bhak, J.8
-
4
-
-
0027145628
-
The pore dimensions of gramicidin a
-
O. S. Smart, J. M. Goodfellow, and B. A. Wallace, "The pore dimensions of gramicidin a," Biophysical Journal, vol. 65, no. 6, pp. 2455-2460, 1993.
-
(1993)
Biophysical Journal
, vol.65
, Issue.6
, pp. 2455-2460
-
-
Smart, O.S.1
Goodfellow, J.M.2
Wallace, B.A.3
-
5
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
O. S. Smart, J. G. Neduvelil, X. Wang, B. A. Wallace, and M. S. P. Sansom, "HOLE: A program for the analysis of the pore dimensions of ion channel structural models," Journal of Molecular Graphics, vol. 14, pp. 354-360, 1996.
-
(1996)
Journal of Molecular Graphics
, vol.14
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
6
-
-
0027995683
-
Detection, delineation, measurement and display of cavities in macromolecular structures
-
G. J. Kleywegt and T. A. Jones, "Detection, delineation, measurement and display of cavities in macromolecular structures," Acta Crystallographica Section D, vol. 50, pp. 178-185, 1994.
-
(1994)
Acta Crystallographica Section D
, vol.50
, pp. 178-185
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
7
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
R. A. Laskowski, "SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions," Journal of Molecular Graphics, vol. 13, pp. 323-330, 1995.
-
(1995)
Journal of Molecular Graphics
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
8
-
-
33745628037
-
The geometry of the ribosomal polypeptide exit tunnel
-
N. R. Voss, M. Gerstein, T. A. Steitz, and P. B. Moore, "The geometry of the ribosomal polypeptide exit tunnel," Journal of Molecular Biology, vol. 260, pp. 893-906, 2006.
-
(2006)
Journal of Molecular Biology
, vol.260
, pp. 893-906
-
-
Voss, N.R.1
Gerstein, M.2
Steitz, T.A.3
Moore, P.B.4
-
9
-
-
33847142225
-
CAVER: A new tool to explore routes from protein clefts, pockets and cavities
-
M. Petrek, M. Otyepka, P. Banas, P. Kosinova, J. Koca, and J. Damborsky, "CAVER: A new tool to explore routes from protein clefts, pockets and cavities," BMC Bioinformatics, vol. 7, no. 316, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.316
-
-
Petrek, M.1
Otyepka, M.2
Banas, P.3
Kosinova, P.4
Koca, J.5
Damborsky, J.6
-
10
-
-
0346945148
-
Pymol: An open-source molecular graphics tool
-
W. L. DeLano, "Pymol: An open-source molecular graphics tool," CCP4 Newsletter, 2002.
-
(2002)
CCP4 Newsletter
-
-
De Lano, W.L.1
-
12
-
-
33847076903
-
Identification of tunnels in proteins, nucleic acids inorganic materials and molecular ensembles
-
J. Damborský, M. Petřek, P. Banáš, and M. Otyepka, "Identification of tunnels in proteins, nucleic acids inorganic materials and molecular ensembles," Biotechnology Journal, vol. 2, pp. 62-67, 2007.
-
(2007)
Biotechnology Journal
, vol.2
, pp. 62-67
-
-
Damborský, J.1
Petřek, M.2
Banáš, P.3
Otyepka, M.4
-
13
-
-
35748972048
-
MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
-
M. Petrek, P. Kosinova, J. Koca, and M. Otyepka, "MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels," Structure, vol. 15, no. 11, pp. 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
-
Computation of tunnels in protein molecules using Delaunay triangulation
-
P. Medek, P. Beneš, and J. Sochor, "Computation of tunnels in protein molecules using Delaunay triangulation," Journal of WSCG, vol. 15, pp. 107-114, 2007.
-
(2007)
Journal of WSCG
, vol.15
, pp. 107-114
-
-
Medek, P.1
Beneš, P.2
Sochor, J.3
-
15
-
-
42149108442
-
Visualization of tunnels in protein molecules
-
B. Kozlíová, F. Andres, and J. Sochor, "Visualization of tunnels in protein molecules," in AfriGraph 2007, 2007, pp. 111-209.
-
(2007)
AfriGraph 2007
, pp. 111-209
-
-
Kozlíová, B.1
Andres, F.2
Sochor, J.3
-
16
-
-
48449083056
-
MolAxis: A server for identification of channels in macromolecules
-
E. Yaffe, D. Fishelovitch, H. J. Wolfson, D. Halperin, and R. Nussinov, "MolAxis: a server for identification of channels in macromolecules," Nucleic Acids Research, vol. 36, pp. W210-W215, 2008.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Yaffe, E.1
Fishelovitch, D.2
Wolfson, H.J.3
Halperin, D.4
Nussinov, R.5
-
17
-
-
50849107731
-
MolAxis: Efficient and accurate identification of channels in macromolecules
-
- "MolAxis: Efficient and accurate identification of channels in macromolecules," Proteins: Structure, Function, and Bioinformatics, vol. 73, no. 1, pp. 72-86, 2008.
-
(2008)
Proteins: Structure, Function, and Bioinformatics
, vol.73
, Issue.1
, pp. 72-86
-
-
Yaffe, E.1
Fishelovitch, D.2
Wolfson, H.J.3
Halperin, D.4
Nussinov, R.5
-
18
-
-
77955773185
-
Approximating the pathway axis and the persistence diagrams for a collection of balls in 3- space
-
E. Yaffe and D. Halperin, "Approximating the pathway axis and the persistence diagrams for a collection of balls in 3- space," Discrete & Computational Geometry, vol. 44, pp. 660-685, 2010.
-
(2010)
Discrete & Computational Geometry
, vol.44
, pp. 660-685
-
-
Yaffe, E.1
Halperin, D.2
-
19
-
-
57649229060
-
HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures
-
B. K. Ho and F. Gruswitz, "HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures," BMC Structural Biology, vol. 8, no. 1, p. 49, 2008.
-
(2008)
BMC Structural Biology
, vol.8
, Issue.1
, pp. 49
-
-
Ho, B.K.1
Gruswitz, F.2
-
20
-
-
58849142521
-
Finding and characterizing tunnels in macromolecules with application to ion channels and pores
-
R. G. Coleman and K. A. Sharp, "Finding and characterizing tunnels in macromolecules with application to ion channels and pores," Biophysical Journal, vol. 96, pp. 632-645, 2009.
-
(2009)
Biophysical Journal
, vol.96
, pp. 632-645
-
-
Coleman, R.G.1
Sharp, K.A.2
-
21
-
-
0003760944
-
-
2nd ed. Chichester: John Wiley & Sons
-
A. Okabe, B. Boots, K. Sugihara, and S. N. Chiu, Spatial Tessellations: Concepts and Applications of Voronoi Diagrams, 2nd ed. Chichester: John Wiley & Sons, 1999.
-
(1999)
Spatial Tessellations: Concepts and Applications of Voronoi Diagrams
-
-
Okabe, A.1
Boots, B.2
Sugihara, K.3
Chiu, S.N.4
-
22
-
-
22944434527
-
Euclidean Voronoi diagram of 3D balls and its computation via tracing edges
-
D.-S. Kim, Y. Cho, and D. Kim, "Euclidean Voronoi diagram of 3D balls and its computation via tracing edges," Computer- Aided Design, vol. 37, no. 13, pp. 1412-1424, 2005.
-
(2005)
Computer- Aided Design
, vol.37
, Issue.13
, pp. 1412-1424
-
-
Kim, D.-S.1
Cho, Y.2
Kim, D.3
-
23
-
-
77955565392
-
Quasi-worlds and quasi-operators on quasi-triangulations
-
D.-S. Kim, Y. Cho, and K. Sugihara, "Quasi-worlds and quasi-operators on quasi-triangulations," Computer-Aided Design, vol. 42, no. 10, pp. 874-888, 2010.
-
(2010)
Computer-Aided Design
, vol.42
, Issue.10
, pp. 874-888
-
-
Kim, D.-S.1
Cho, Y.2
Sugihara, K.3
-
24
-
-
33745813533
-
Quasitriangulation and interworld data structure in three dimensions
-
D.-S. Kim, D. Kim, Y. Cho, and K. Sugihara, "Quasitriangulation and interworld data structure in three dimensions," Computer-Aided Design, vol. 38, no. 7, pp. 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
-
25
-
-
77955569416
-
Threedimensional beta-shapes and beta-complexes via quasitriangulation
-
D.-S. Kim, Y. Cho, K. Sugihara, J. Ryu, and D. Kim, " Threedimensional beta-shapes and beta-complexes via quasitriangulation," Computer-Aided Design, vol. 42, no. 10, pp. 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
-
27
-
-
20544433165
-
Van der Waals volumes and radii
-
A. Bondi, "van der Waals volumes and radii," Journal of Physical Chemistry, vol. 68, pp. 441-451, 1964.
-
(1964)
Journal of Physical Chemistry
, vol.68
, pp. 441-451
-
-
Bondi, A.1
-
28
-
-
84862776651
-
Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets
-
DOI: 10.1002/jcc.22956
-
D.-S. Kim, J. Ryu, H. Shin, and Y. Cho, "Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets," Journal of Computational Chemistry, vol. (DOI: 10.1002/jcc.22956), 2011.
-
(2011)
Journal of Computational Chemistry
-
-
Kim, D.-S.1
Ryu, J.2
Shin, H.3
Cho, Y.4
|