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Volumn 15, Issue 11, 2007, Pages 1357-1363

MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLCHOLINESTERASE; CYTOCHROME P450; GRAMICIDIN; POTASSIUM CHANNEL;

EID: 35748972048     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.10.007     Document Type: Article
Times cited : (206)

References (50)
  • 1
    • 0029151790 scopus 로고
    • Aquaporin water channels-unanswered questions and unresolved controversies
    • Agre P., Brown D., and Nielsen S. Aquaporin water channels-unanswered questions and unresolved controversies. Curr. Opin. Cell Biol. 7 (1995) 472-483
    • (1995) Curr. Opin. Cell Biol. , vol.7 , pp. 472-483
    • Agre, P.1    Brown, D.2    Nielsen, S.3
  • 2
    • 0023287929 scopus 로고
    • Power diagrams-properties, algorithms and applications
    • Aurenhammer F. Power diagrams-properties, algorithms and applications. SIAM J. Comput. 16 (1987) 78-96
    • (1987) SIAM J. Comput. , vol.16 , pp. 78-96
    • Aurenhammer, F.1
  • 3
    • 6244277276 scopus 로고
    • Geometric relations among Voronoi diagrams
    • Springer-Verlag, Passau, Germany
    • Aurenhammer F., and Imai H. Geometric relations among Voronoi diagrams. Lecture Notes in Computer Science Volume 247 (1987), Springer-Verlag, Passau, Germany 53-65
    • (1987) Lecture Notes in Computer Science , vol.247 , pp. 53-65
    • Aurenhammer, F.1    Imai, H.2
  • 7
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • Brady G.P., and Stouten P.F.W. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 14 (2000) 383-401
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 383-401
    • Brady, G.P.1    Stouten, P.F.W.2
  • 10
    • 33847076903 scopus 로고    scopus 로고
    • Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
    • Damborsky J., Petrek M., Banas P., and Otyepka M. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnol. J. 2 (2007) 62-67
    • (2007) Biotechnol. J. , vol.2 , pp. 62-67
    • Damborsky, J.1    Petrek, M.2    Banas, P.3    Otyepka, M.4
  • 11
    • 34147120474 scopus 로고
    • A note on two problems in connection with graphs
    • Dijkstra E.W. A note on two problems in connection with graphs. Numerische Mathematik 1 (1959) 83-89
    • (1959) Numerische Mathematik , vol.1 , pp. 83-89
    • Dijkstra, E.W.1
  • 13
    • 51249175171 scopus 로고
    • Higher-dimensional Voronoi diagrams in linear expected time
    • Dwyer R.A. Higher-dimensional Voronoi diagrams in linear expected time. Discrete Comput. Geom. 6 (1991) 343-367
    • (1991) Discrete Comput. Geom. , vol.6 , pp. 343-367
    • Dwyer, R.A.1
  • 14
    • 0002052671 scopus 로고    scopus 로고
    • On the definition and the construction of pockets in macromolecules
    • Edelsbrunner H., Facello M., and Liang J. On the definition and the construction of pockets in macromolecules. Discrete Appl. Math. 88 (1998) 83-102
    • (1998) Discrete Appl. Math. , vol.88 , pp. 83-102
    • Edelsbrunner, H.1    Facello, M.2    Liang, J.3
  • 15
    • 0028170113 scopus 로고
    • The aquaporin family of membrane water channels
    • Engel A., Walz T., and Agre P. The aquaporin family of membrane water channels. Curr. Opin. Struct. Biol. 4 (1994) 545-553
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 545-553
    • Engel, A.1    Walz, T.2    Agre, P.3
  • 16
    • 0034161393 scopus 로고    scopus 로고
    • The importance of aquaporin water channel protein structures
    • Engel A., Fijiyoshi Y., and Agre P. The importance of aquaporin water channel protein structures. EMBO J. 19 (2000) 800-806
    • (2000) EMBO J. , vol.19 , pp. 800-806
    • Engel, A.1    Fijiyoshi, Y.2    Agre, P.3
  • 17
    • 35748970618 scopus 로고    scopus 로고
    • Garber, M., and Lin, M.C. (2002). Constraint-based motion planning using Voronoi diagrams. Proc. Fifth International Workshop on Algorithmic Foundations of Robotics (WAFR).
  • 18
    • 28544453561 scopus 로고    scopus 로고
    • Principles of selective ion transport in channels and pumps
    • Gouaux E., and MacKinnon R. Principles of selective ion transport in channels and pumps. Science 310 (2005) 1461-1465
    • (2005) Science , vol.310 , pp. 1461-1465
    • Gouaux, E.1    MacKinnon, R.2
  • 19
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M., Rippmann F., and Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 15 (1997) 359-364
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 359-364
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 20
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang B.D., and Schroeder M. LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 6 (2006) 19
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.D.1    Schroeder, M.2
  • 21
    • 0037198626 scopus 로고    scopus 로고
    • Crystal structure and mechanism of a calcium-gated potassium channel
    • Jiang Y.X., Lee A., Chen J.Y., Cadene M., Chait B.T., and MacKinnon R. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417 (2002) 515-522
    • (2002) Nature , vol.417 , pp. 515-522
    • Jiang, Y.X.1    Lee, A.2    Chen, J.Y.3    Cadene, M.4    Chait, B.T.5    MacKinnon, R.6
  • 24
    • 22944434527 scopus 로고    scopus 로고
    • Euclidean Voronoi diagram of 3D balls and its computation via tracing edges
    • Kim D.S., Cho Y., and Kim D. Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Comput. Aided Des. 37 (2005) 1412-1424
    • (2005) Comput. Aided Des. , vol.37 , pp. 1412-1424
    • Kim, D.S.1    Cho, Y.2    Kim, D.3
  • 25
    • 0035423087 scopus 로고    scopus 로고
    • The kink-turn: a new RNA secondary structure motif
    • Klein D.J., Schmeing T.M., Moore P.B., and Steitz T.A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20 (2001) 4214-4221
    • (2001) EMBO J. , vol.20 , pp. 4214-4221
    • Klein, D.J.1    Schmeing, T.M.2    Moore, P.B.3    Steitz, T.A.4
  • 26
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt G.J., and Jones T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 178-185
    • (1994) Acta Crystallogr. D Biol. Crystallogr. , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 27
    • 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. J. Mol. Graph. 13 (1995) 323-325
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-325
    • Laskowski, R.A.1
  • 28
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • Laurie A.T.R., and Jackson R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21 (2005) 1908-1916
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 29
    • 24544471449 scopus 로고
    • Molecular speleology-the exploration of crevices in proteins for prediction of binding-sites, design of drugs and analysis of surface recognition
    • Lesk A.M. Molecular speleology-the exploration of crevices in proteins for prediction of binding-sites, design of drugs and analysis of surface recognition. Acta Crystallogr. A 42 (1986) 83-85
    • (1986) Acta Crystallogr. A , vol.42 , pp. 83-85
    • Lesk, A.M.1
  • 30
    • 0027053611 scopus 로고
    • Pocket: a computer-graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • Levitt D.G., and Banaszak L.J. Pocket: a computer-graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph. 10 (1992) 229-234
    • (1992) J. Mol. Graph. , vol.10 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 33
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design
    • Liang J., Edelsbrunner H., and Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7 (1998) 1884-1897
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 34
    • 0037149513 scopus 로고    scopus 로고
    • Nothing automatic about ion-channel structures
    • MacKinnon R. Nothing automatic about ion-channel structures. Nature 416 (2002) 261-262
    • (2002) Nature , vol.416 , pp. 261-262
    • MacKinnon, R.1
  • 35
    • 0242657337 scopus 로고    scopus 로고
    • Potassium channels
    • MacKinnon R. Potassium channels. FEBS Lett. 555 (2003) 62-65
    • (2003) FEBS Lett. , vol.555 , pp. 62-65
    • MacKinnon, R.1
  • 36
    • 33846380189 scopus 로고    scopus 로고
    • What common structural features and variations of mammalian P450s are known to date?
    • Otyepka M., Skopalik J., Anzenbacherova E., and Anzenbacher P. What common structural features and variations of mammalian P450s are known to date?. Biochim. Biophys. Acta 1770 (2007) 376-389
    • (2007) Biochim. Biophys. Acta , vol.1770 , pp. 376-389
    • Otyepka, M.1    Skopalik, J.2    Anzenbacherova, E.3    Anzenbacher, P.4
  • 39
    • 1842850600 scopus 로고    scopus 로고
    • Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
    • Poupon A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opin. Struct. Biol. 14 (2004) 233-241
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 233-241
    • Poupon, A.1
  • 40
    • 0015977588 scopus 로고
    • The interpretation of protein structures: total volume, group volume distributions and packing density
    • Richards F.M. The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82 (1974) 1-14
    • (1974) J. Mol. Biol. , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 42
    • 0030404988 scopus 로고    scopus 로고
    • 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. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. Model. 14 (1996) 354-360
    • (1996) J. Mol. Graph. Model. , 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
  • 43
    • 33645344882 scopus 로고    scopus 로고
    • Mesopore-modified zeolites: preparation, characterization, and applications
    • Tao Y.S., Kanoh H., Abrams L., and Kaneko K. Mesopore-modified zeolites: preparation, characterization, and applications. Chem. Rev. 106 (2006) 896-910
    • (2006) Chem. Rev. , vol.106 , pp. 896-910
    • Tao, Y.S.1    Kanoh, H.2    Abrams, L.3    Kaneko, K.4
  • 44
    • 33745628037 scopus 로고    scopus 로고
    • The geometry of the ribosomal polypeptide exit tunnel
    • Voss N.R., Gerstein M., Steitz T.A., and Moore P.B. The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol. 360 (2006) 893-906
    • (2006) J. Mol. Biol. , vol.360 , pp. 893-906
    • Voss, N.R.1    Gerstein, M.2    Steitz, T.A.3    Moore, P.B.4
  • 45
    • 3042587451 scopus 로고    scopus 로고
    • A survey of active site access channels in cytochromes P450
    • Wade R.C., Winn P.J., Schlichting E., and Sudarko. A survey of active site access channels in cytochromes P450. J. Inorg. Biochem. 98 (2004) 1175-1182
    • (2004) J. Inorg. Biochem. , vol.98 , pp. 1175-1182
    • Wade, R.C.1    Winn, P.J.2    Schlichting, E.3    Sudarko4
  • 47
    • 0028275784 scopus 로고
    • The 3-dimensional structure of human erythrocyte aquaporin chip
    • Walz T., Smith B.L., Agre P., and Engel A. The 3-dimensional structure of human erythrocyte aquaporin chip. EMBO J. 13 (1994) 2985-2993
    • (1994) EMBO J. , vol.13 , pp. 2985-2993
    • Walz, T.1    Smith, B.L.2    Agre, P.3    Engel, A.4
  • 50
    • 0035499892 scopus 로고    scopus 로고
    • Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 angstrom resolution
    • Zhou Y.F., Morais-Cabral J.H., Kaufman A., and MacKinnon R. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 angstrom resolution. Nature 414 (2001) 43-48
    • (2001) Nature , vol.414 , pp. 43-48
    • Zhou, Y.F.1    Morais-Cabral, J.H.2    Kaufman, A.3    MacKinnon, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.