-
1
-
-
84871936785
-
Software tools for identification, visualization and analysis of protein tunnels and channels
-
Brezovskya, J., Chovancova, E., Gora, A., Pavelka, A., Biedermannova, L. and Damborsky, J. (2013) Software tools for identification, visualization and analysis of protein tunnels and channels. Biotechnol. Adv., 31, 38-49.
-
(2013)
Biotechnol. Adv.
, vol.31
, pp. 38-49
-
-
Brezovskya, J.1
Chovancova, E.2
Gora, A.3
Pavelka, A.4
Biedermannova, L.5
Damborsky, J.6
-
2
-
-
84921791027
-
Detection of intramolecular tunnels connecting sequence of sites in protein structures
-
Strnad, O., Kozlikova, B. and Sochor, J. (2014) Detection of intramolecular tunnels connecting sequence of sites in protein structures. Adv. Intell. Syst. Comput., 294, 73-80.
-
(2014)
Adv. Intell. Syst. Comput.
, vol.294
, pp. 73-80
-
-
Strnad, O.1
Kozlikova, B.2
Sochor, J.3
-
3
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
Connolly, M.L. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
4
-
-
33845377446
-
Computation of molecular volume
-
Connolly, M.L. (1985) Computation of molecular volume. J. Am. Chem. Soc., 107, 1118-1124.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 1118-1124
-
-
Connolly, M.L.1
-
5
-
-
0027995683
-
Detection, delineation, measurement and display of cavities in macromolecular structures
-
Kleywegt, G.J. and Jones, T.A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D, 50, 178-185.
-
(1994)
Acta Crystallogr. D
, vol.50
, pp. 178-185
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
6
-
-
9244229562
-
Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein
-
Cuff, A.L. and Martin, A.C.R. (2004) Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein. J. Mol. Biol., 344, 1199-1209.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1199-1209
-
-
Cuff, A.L.1
Martin, A.C.R.2
-
7
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski, R.A. (1995) SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330.
-
(1995)
J. Mol. Graph.
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
8
-
-
77957296071
-
Rosetta holes2: A volumetric packing measure for protein structure refinement and validation
-
Sheffler, W. and Baker, D. (2010) Rosetta Holes2: a volumetric packing measure for protein structure refinement and validation. Protein Sci., 19, 1991-1995.
-
(2010)
Protein Sci.
, vol.19
, pp. 1991-1995
-
-
Sheffler, W.1
Baker, D.2
-
9
-
-
0032190305
-
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
-
Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V. and Subramaniam, S. (1998) Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins, 33, 1-17.
-
(1998)
Proteins
, vol.33
, pp. 1-17
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
10
-
-
33747818007
-
CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y. and Liang, J. (2006) CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res., 34, W116-W118.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W116-W118
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
Liang, J.6
-
11
-
-
84906314324
-
Beta void: Molecular voids via beta-complexes and voronoi diagrams
-
Kim, J.-K., Cho, Y., Laskowski, R.A., Ryu, S.E., Sugihara, K. and Kim, D.-S. (2014) Beta Void: molecular voids via beta-complexes and Voronoi diagrams. Proteins, 82, 1829-1849.
-
(2014)
Proteins
, vol.82
, pp. 1829-1849
-
-
Kim, J.-K.1
Cho, Y.2
Laskowski, R.A.3
Ryu, S.E.4
Sugihara, K.5
Kim, D.-S.6
-
12
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A. and Sansom, M.S.P. (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph., 14, 354-360.
-
(1996)
J. Mol. Graph.
, 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
-
13
-
-
33745628037
-
The geometry of the ribosomal polypeptide exit tunnel
-
Voss, N.R., Gerstein, M., Steitz, T.A. and Moore, P.B. (2006) The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol., 260, 893-906.
-
(2006)
J. Mol. Biol.
, vol.260
, pp. 893-906
-
-
Voss, N.R.1
Gerstein, M.2
Steitz, T.A.3
Moore, P.B.4
-
14
-
-
34548519907
-
A 30 Å long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase
-
Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P. and Mattevi, A. (1999) A 30 Å long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Structure, 7, 265-276.
-
(1999)
Structure
, vol.7
, pp. 265-276
-
-
Binda, C.1
Coda, A.2
Angelini, R.3
Federico, R.4
Ascenzi, P.5
Mattevi, A.6
-
15
-
-
0034702177
-
Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
-
Koronakis, V., Sharff, A., Koronakis, E., Luisi, B. and Hughes, C. (2000) Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature, 405, 914-919.
-
(2000)
Nature
, vol.405
, pp. 914-919
-
-
Koronakis, V.1
Sharff, A.2
Koronakis, E.3
Luisi, B.4
Hughes, C.5
-
16
-
-
28544453561
-
Principles of selective ion transport in channels and pumps
-
Gouaux, E. and MacKinnon, R. (2005) Principles of selective ion transport in channels and pumps. Science, 310, 1461-1465.
-
(2005)
Science
, vol.310
, pp. 1461-1465
-
-
Gouaux, E.1
MacKinnon, R.2
-
17
-
-
41149095488
-
How membrane proteins sense voltage
-
Bezanilla, F. (2005) How membrane proteins sense voltage. Nat. Rev. Mol. Cell Biol., 9, 323-332.
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.9
, pp. 323-332
-
-
Bezanilla, F.1
-
19
-
-
33847142225
-
CAVER: A new tool to explore routes from protein clefts, pockets and cavities
-
Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J. and Damborsky, J. (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform.,7, 316.
-
(2006)
BMC Bioinform
, vol.7
, pp. 316
-
-
Petrek, M.1
Otyepka, M.2
Banas, P.3
Kosinova, P.4
Koca, J.5
Damborsky, J.6
-
21
-
-
35748972048
-
MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
-
Petrek, M., Kosinova, P., Koca, J. and Otyepka, M. (2007) MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15, 1357-1363.
-
(2007)
Structure
, vol.15
, pp. 1357-1363
-
-
Petrek, M.1
Kosinova, P.2
Koca, J.3
Otyepka, M.4
-
22
-
-
48449083056
-
Mol axis: A server for identification of channels in macromolecules
-
Yaffe, E., Fishelovitch, D., Wolfson, H.J., Halperin, D. and Nussinov, R. (2008) Mol Axis: a server for identification of channels in macromolecules. Nucleic Acids Res., 36, W210-W215.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W210-W215
-
-
Yaffe, E.1
Fishelovitch, D.2
Wolfson, H.J.3
Halperin, D.4
Nussinov, R.5
-
23
-
-
68249097450
-
Pore walker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure
-
Pellegrini-Calace, M., Maiwald, T. and Thornton, J.M. (2009) Pore Walker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput. Biol., 5, e1000440.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000440
-
-
Pellegrini-Calace, M.1
Maiwald, T.2
Thornton, J.M.3
-
24
-
-
80855130019
-
Member, Voronoi-based extraction and visualization of molecular paths
-
Norbert Lindow, D.B. and Hans-Christian Hege, I. (2011) Member, Voronoi-based extraction and visualization of molecular paths. IEEE Trans. Vis. Comput. Graph., 17, 2025-2034.
-
(2011)
IEEE Trans. Vis. Comput. Graph.
, vol.17
, pp. 2025-2034
-
-
Norbert Lindow, D.B.1
Hans-Christian Hege, I.2
-
25
-
-
22944434527
-
Euclidean voronoi diagram of 3D balls and its computation via tracing edges
-
Kim, D.-S., Cho, Y. and Kim, D. (2006) Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Comput. Aided Des., 37, 1412-1424.
-
(2006)
Comput. Aided Des.
, vol.37
, pp. 1412-1424
-
-
Kim, D.-S.1
Cho, Y.2
Kim, D.3
-
26
-
-
84864486886
-
MOLEonline 2.0: Interactive web-based analysis of biomacromolecular channels
-
Berka, K., Hanák, O., Sehnal, D., Banáš, P., Navrátilová, V., Jaiswal, D., Ionescu, C.-M., Vařeková, R.S., Koča, J. and Otyepka, M. (2012) MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res., 40, W222-W227.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W222-W227
-
-
Berka, K.1
Hanák, O.2
Sehnal, D.3
Banáš, P.4
Navrátilová, V.5
Jaiswal, D.6
Ionescu, C.-M.7
Vařeková, R.S.8
Koča, J.9
Otyepka, M.10
-
27
-
-
84868156224
-
CAVER 3.0: A tool for the analysis of transport pathways in dynamic protein structures
-
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P. et al. (2012) CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput. Biol., 8, e1002708.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002708
-
-
Chovancova, E.1
Pavelka, A.2
Benes, P.3
Strnad, O.4
Brezovsky, J.5
Kozlikova, B.6
Gora, A.7
Sustr, V.8
Klvana, M.9
Medek, P.10
-
28
-
-
0033555677
-
A correlation between the loss of hydrophobic core packing interactions and protein stability
-
Vlassi, M., Cesareni, G. and Kokkinidis, M. (1999) A correlation between the loss of hydrophobic core packing interactions and protein stability. J. Mol. Biol., 285, 817-827.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 817-827
-
-
Vlassi, M.1
Cesareni, G.2
Kokkinidis, M.3
-
29
-
-
0028274954
-
Intramolecular cavities in globular proteins
-
Hubbard, S.J., Gross, K.-H. and Argos, P. (1994) Intramolecular cavities in globular proteins. Protein Eng., 7, 613-626.
-
(1994)
Protein Eng.
, vol.7
, pp. 613-626
-
-
Hubbard, S.J.1
Gross, K.-H.2
Argos, P.3
-
30
-
-
84926451475
-
Side-chain prediction and computational protein design problems
-
Kim, D.-S. and Ryu, J. (2014) Side-chain prediction and computational protein design problems. Biodesign, 2, 26-38.
-
(2014)
Biodesign
, vol.2
, pp. 26-38
-
-
Kim, D.-S.1
Ryu, J.2
-
32
-
-
0037840702
-
Updating the topology of the dynamic Voronoi diagram for spheres in Euclidean d-dimensional space
-
Gavrilova, M. and Rokne, J. (2003) Updating the topology of the dynamic Voronoi diagram for spheres in Euclidean d-dimensional space. Comput. Aided Geometric Des., 20, 231-242.
-
(2003)
Comput. Aided Geometric Des.
, vol.20
, pp. 231-242
-
-
Gavrilova, M.1
Rokne, J.2
-
33
-
-
0003760944
-
-
2nd ed. John Wiley & Sons, Chichester
-
Okabe, A., Boots, B., Sugihara, K. and Chiu, S.N. (1999) Spatial Tessellations: Concepts and Applications of Voronoi Diagrams, 2nd ed. John Wiley & Sons, Chichester.
-
(1999)
Spatial Tessellations: Concepts and Applications of Voronoi Diagrams
-
-
Okabe, A.1
Boots, B.2
Sugihara, K.3
Chiu, S.N.4
-
34
-
-
33745813533
-
Quasi-triangulation and interworld data structure in three dimensions
-
Kim, D.-S., Kim, D., Cho, Y. and Sugihara, K. (2006) Quasi-triangulation and interworld data structure in three dimensions. Comput. Aided Des., 38, 808-819.
-
(2006)
Comput. Aided Des.
, vol.38
, pp. 808-819
-
-
Kim, D.-S.1
Kim, D.2
Cho, Y.3
Sugihara, K.4
-
35
-
-
77955565392
-
Quasi-worlds and quasi-operators on quasi-triangulations
-
Kim, D.-S., Cho, Y. and Sugihara, K. (2010) Quasi-worlds and quasi-operators on quasi-triangulations. Comput. Aided Des., 42, 874-888.
-
(2010)
Comput. Aided Des.
, vol.42
, pp. 874-888
-
-
Kim, D.-S.1
Cho, Y.2
Sugihara, K.3
-
36
-
-
84867663377
-
Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules
-
Kim, D.-S., Cho, Y., Ryu, J., Kim, J.-K. and Kim, D. (2013) Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules. Comput. Aided Des., 45, 35-52.
-
(2013)
Comput. Aided Des.
, vol.45
, pp. 35-52
-
-
Kim, D.-S.1
Cho, Y.2
Ryu, J.3
Kim, J.-K.4
Kim, D.5
-
37
-
-
77955569416
-
Three-dimensional beta-shapes and beta-complexes via quasi-triangulation
-
Kim, D.-S., Cho, Y., Sugihara, K., Ryu, J. and Kim, D. (2010) Three-dimensional beta-shapes and beta-complexes via quasi-triangulation. Comput. Aided Des., 42, 911-929.
-
(2010)
Comput. Aided Des.
, vol.42
, pp. 911-929
-
-
Kim, D.-S.1
Cho, Y.2
Sugihara, K.3
Ryu, J.4
Kim, D.5
-
39
-
-
84892778855
-
Tunnels and voids in molecules via Voronoi diagrams and beta-complexes
-
LNCS
-
Kim, D.-S., Cho, Y., Kim, J.-K. and Sugihara, K. (2013) Tunnels and voids in molecules via Voronoi diagrams and beta-complexes. Trans. Comput. Sci. XX, LNCS 8110, 92-111.
-
(2013)
Trans. Comput. Sci. XX
, vol.8110
, pp. 92-111
-
-
Kim, D.-S.1
Cho, Y.2
Kim, J.-K.3
Sugihara, K.4
-
40
-
-
84892737367
-
Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets
-
Kim, D.-S., Ryu, J., Shin, H. and Cho, Y. (2012) Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets. J. Comput. Chem., 12, 1225-1283.
-
(2012)
J. Comput. Chem.
, vol.12
, pp. 1225-1283
-
-
Kim, D.-S.1
Ryu, J.2
Shin, H.3
Cho, Y.4
-
41
-
-
84984697061
-
-
(1 April, date last accessed)
-
RCSB Protein Data Bank. http://www.rcsb.org/pdb/, (1 April 2014, date last accessed).
-
(2014)
-
-
-
42
-
-
0035859892
-
Crystal structure of the dimeric extracellular domain of human carbonic anhydrase xii, a bitopic membrane protein overexpressed in certain cancer tumor cells
-
Whittington, D.A., Waheed, A., Ulmasov, B., Shah, G.N., Grubb, J.H., Sly, W.S. and Christianson, D.W. (2001) Crystal structure of the dimeric extracellular domain of human carbonic anhydrase xii, a bitopic membrane protein overexpressed in certain cancer tumor cells. Proc. Natl. Acad. Sci., 98, 9545-9550.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 9545-9550
-
-
Whittington, D.A.1
Waheed, A.2
Ulmasov, B.3
Shah, G.N.4
Grubb, J.H.5
Sly, W.S.6
Christianson, D.W.7
-
43
-
-
72249101494
-
Structural insights into the substrate tunnel of saccharomyces cerevisiae carbonic anhydrase nce103
-
Teng, Y.-B., Jiang, Y.-L., He, Y.-X., He, W.-W., Lian, F.-M., Chen, Y. and Zhou, C.-Z. (2009) Structural insights into the substrate tunnel of saccharomyces cerevisiae carbonic anhydrase nce103. Biomed Cent. Struct. Biol., 9, 1-8.
-
(2009)
Biomed Cent. Struct. Biol.
, vol.9
, pp. 1-8
-
-
Teng, Y.-B.1
Jiang, Y.-L.2
He, Y.-X.3
He, W.-W.4
Lian, F.-M.5
Chen, Y.6
Zhou, C.-Z.7
-
44
-
-
84984697079
-
-
(1 April, date last accessed)
-
JSmol: an open-source HTML5 viewer for chemical structures in 3D. http://wiki.jmol.org/index.php/JSmol, (1 April 2014, date last accessed).
-
(2014)
-
-
-
45
-
-
84861795172
-
QTF: Quasi-triangulation file format
-
Kim, D.-S., Cho, Y., Kim, J.-K. and Ryu, J. (2012) QTF: Quasi-triangulation file format. Comput. Aided Des., 44, 835-845.
-
(2012)
Comput. Aided Des.
, vol.44
, pp. 835-845
-
-
Kim, D.-S.1
Cho, Y.2
Kim, J.-K.3
Ryu, J.4
|