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Volumn , Issue , 2012, Pages 99-106

Dynamic channels in biomolecular systems: Path analysis and visualization

Author keywords

I.3.5 Computer Graphics : Comput. Geom. Object Modeling Boundary Representations; J.3 Computer Applications : Life and Medical Sciences Biology and Genetics

Indexed keywords

BIOMOLECULAR SYSTEM; CAVITY DYNAMICS; CAVITY STRUCTURE; DYNAMIC STRUCTURE; INTERNAL CAVITIES; LIFE AND MEDICAL SCIENCE; MOLECULAR DYNAMICS TRAJECTORIES; OBJECT MODELING; PATH ANALYSIS; PRE-PROCESSING STEP; PROTEIN DYNAMICS; PROTON PUMP; SINGLE IMAGES; SPECIFIC COMPONENT; STRUCTURE AND DYNAMICS; TIME EVOLUTIONS; TIME-DEPENDENT; VAN DER WAALS; VISUALIZATION METHOD; VISUALIZATION TECHNIQUE; VISUALIZATION TOOLS; VORONOI DIAGRAMS;

EID: 84872252594     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BioVis.2012.6378599     Document Type: Conference Paper
Times cited : (27)

References (64)
  • 1
    • 69849114705 scopus 로고    scopus 로고
    • Structural dynamics of light-driven proton pumps original research article structure
    • M. Andersson, E. Malmerberg, S. Westenhoff, and G. Katona et al. Structural dynamics of light-driven proton pumps original research article structure. Structure, 17(9):1265-1275, 2009.
    • (2009) Structure , vol.17 , Issue.9 , pp. 1265-1275
    • Andersson, M.1    Malmerberg, E.2    Westenhoff, S.3    Katona, G.4
  • 2
    • 0033567092 scopus 로고    scopus 로고
    • Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 Å resolution
    • H. Belrhali, P. Nollert, and A. Royant et al. Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 Å resolution. Structure, 7(8):909-917, 1999.
    • (1999) Structure , vol.7 , Issue.8 , pp. 909-917
    • Belrhali, H.1    Nollert, P.2    Royant, A.3
  • 3
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed atlas of surface topography of proteins
    • T. Binkowski, S. Naghibzadeh, and J. Liang. CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Res., 31(13):3352-5, 2003.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.13 , pp. 3352-3355
    • Binkowski, T.1    Naghibzadeh, S.2    Liang, J.3
  • 4
    • 84862168074 scopus 로고    scopus 로고
    • Extended protein/water h-bond networks in photosynthetic water oxidation
    • A.-N. Bondar and H. Dau. Extended protein/water h-bond networks in photosynthetic water oxidation. BBA-Bioenergetics, 2012.
    • (2012) BBA-Bioenergetics
    • Bondar, A.-N.1    Dau, H.2
  • 5
    • 79955667818 scopus 로고    scopus 로고
    • Water pathways in the bacteriorhodopsin proton pump
    • A.-N. Bondar, S. Fischer, and J. Smith. Water pathways in the bacteriorhodopsin proton pump. J. Membr. Biol., 239:73-84, 2011.
    • (2011) J. Membr. Biol. , vol.239 , pp. 73-84
    • Bondar, A.-N.1    Fischer, S.2    Smith, J.3
  • 8
    • 68249097450 scopus 로고    scopus 로고
    • PoreWalker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure
    • M. P. Calace, T. Maiwald, and J. M. Thornton. PoreWalker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput. Biol., 5(7), 2009.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.7
    • Calace, M.P.1    Maiwald, T.2    Thornton, J.M.3
  • 9
    • 58849142521 scopus 로고    scopus 로고
    • 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. Biophys. J., 96:632-645, 2008.
    • (2008) Biophys. J. , vol.96 , pp. 632-645
    • Coleman, R.G.1    Sharp, K.A.2
  • 10
    • 29144467680 scopus 로고    scopus 로고
    • A path planning approach for computing large-amplitude motions of flexible molecules
    • J. Cortés, T. Siméon, V. De Angulo, D. Guieysse, M. Remaud-Siméon, and V. Tran. A path planning approach for computing large-amplitude motions of flexible molecules. Bioinformatics, 21(suppl 1):i116-i125, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Cortés, J.1    Siméon, T.2    De Angulo, V.3    Guieysse, D.4    Remaud-Siméon, M.5    Tran, V.6
  • 11
    • 33846823909 scopus 로고
    • Particle mesh ewald: An n log(n) method for ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen. Particle mesh ewald: an n log(n) method for ewald sums in large systems. J. Chem. Phys., 98:10089-10092, 1993.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 12
    • 77953080085 scopus 로고    scopus 로고
    • Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations
    • R. O. Dror, M. Jensen, D. W. Borhani, and D. E. Shaw. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J. Gen. Physiol., 135(6):555-562, 2010.
    • (2010) J. Gen. Physiol. , vol.135 , Issue.6 , pp. 555-562
    • Dror, R.O.1    Jensen, M.2    Borhani, D.W.3    Shaw, D.E.4
  • 13
    • 0033482642 scopus 로고    scopus 로고
    • Deformable smooth surface design
    • H. Edelsbrunner. Deformable smooth surface design. Discrete Comput. Geom., 21(1):87-115, 1999.
    • (1999) Discrete Comput. Geom. , vol.21 , Issue.1 , pp. 87-115
    • Edelsbrunner, H.1
  • 16
    • 0038592455 scopus 로고    scopus 로고
    • Identification of substrate channels and protein cavities
    • T. Exner, M. Keil, G. Möckel, and J. Brickmann. Identification of substrate channels and protein cavities. J. Mol. Model., 4:340-343, 1998.
    • (1998) J. Mol. Model. , vol.4 , pp. 340-343
    • Exner, T.1    Keil, M.2    Möckel, G.3    Brickmann, J.4
  • 17
    • 0034250744 scopus 로고    scopus 로고
    • An improved empirical potential energy function for molecular simulations of phospholipids
    • S. Feller and A. MacKerell Jr. An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B, 104:7510-7515, 2000.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7510-7515
    • Feller, S.1    MacKerell Jr., A.2
  • 18
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • S. Feller, Y. Zhang, R. Pastor, and B. Brooks. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys., 103:4613-4621, 1995.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.1    Zhang, Y.2    Pastor, R.3    Brooks, B.4
  • 19
    • 84963146276 scopus 로고
    • Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    • H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul., 6:121-142, 1991.
    • (1991) Mol. Simul. , vol.6 , pp. 121-142
    • Grubmüller, H.1    Heller, H.2    Windemuth, A.3    Schulten, K.4
  • 20
    • 17844397460 scopus 로고    scopus 로고
    • Water molecules and hydrogen-bonded networks in bacteriorhodopsin - Molecular dynamics simulations of the ground state and the m-intermediate
    • S. Grudinin, G. Büldt, V. Gordeliy, and A. Baumgaertner. Water molecules and hydrogen-bonded networks in bacteriorhodopsin - molecular dynamics simulations of the ground state and the m-intermediate. Biophys. J., 88(5):3252-3261, 2005.
    • (2005) Biophys. J. , vol.88 , Issue.5 , pp. 3252-3261
    • Grudinin, S.1    Büldt, G.2    Gordeliy, V.3    Baumgaertner, A.4
  • 21
    • 17044402537 scopus 로고    scopus 로고
    • Mechanism of a molecular valve in the halorhodopsin chloride pump
    • A. D. Gruia, A.-N. Bondar, J. C. Smith, and S. Fischer. Mechanism of a molecular valve in the halorhodopsin chloride pump. Structure, 13(4):617-627, 2005.
    • (2005) Structure , vol.13 , Issue.4 , pp. 617-627
    • Gruia, A.D.1    Bondar, A.-N.2    Smith, J.C.3    Fischer, S.4
  • 23
    • 57649229060 scopus 로고    scopus 로고
    • 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 Struct. Biol., 8(1):49+, 2008.
    • (2008) BMC Struct. Biol. , vol.8 , Issue.1
    • Ho, B.K.1    Gruswitz, F.2
  • 24
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    • B. Huang and M. Schroeder. LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol., 6(1):19, 2006.
    • (2006) BMC Struct. Biol. , vol.6 , Issue.1 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 25
    • 77958499673 scopus 로고    scopus 로고
    • Coupling of retinal, protein, and water dynamics in squid rhodopsin
    • E. Jardón-Valadez, A.-N. Bondar, and D. J. Tobias. Coupling of retinal, protein, and water dynamics in squid rhodopsin. Biophys. J., 99(7):2200-2207, 2010.
    • (2010) Biophys. J. , vol.99 , Issue.7 , pp. 2200-2207
    • Jardón-Valadez, E.1    Bondar, A.-N.2    Tobias, D.J.3
  • 27
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with pass
    • G. P. B. Jr. and P. F. W. Stouten. Fast prediction and visualization of protein binding pockets with pass. J. Comput-Aided Mol. Des., 14(4):383-401, 2000.
    • (2000) J. Comput-Aided Mol. Des. , vol.14 , Issue.4 , pp. 383-401
    • B Jr., G.P.1    Stouten, P.F.W.2
  • 28
    • 0042415783 scopus 로고    scopus 로고
    • NAMD2: Greater scalability for parallel molecular dynamics
    • L. Kale, R. Skeel, M. Bhandarkar, and R. Brunner et al. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys., 151:283-312, 1999.
    • (1999) J. Comput. Phys. , vol.151 , pp. 283-312
    • Kale, L.1    Skeel, R.2    Bhandarkar, M.3    Brunner, R.4
  • 29
    • 22944434527 scopus 로고    scopus 로고
    • 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. Comput. Aided Des., 37(13):1412-1424, 2005.
    • (2005) Comput. Aided Des. , vol.37 , Issue.13 , pp. 1412-1424
    • Kim, D.-S.1    Cho, Y.2    Kim, D.3
  • 30
    • 0027995683 scopus 로고
    • 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 Crystallogr. D, 50(2):178-185, 1994.
    • (1994) Acta Crystallogr. D , vol.50 , Issue.2 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 31
    • 70350635971 scopus 로고    scopus 로고
    • Interactive visualization of molecular surface dynamics
    • M. Krone, K. Bidmon, and T. Ertl. Interactive visualization of molecular surface dynamics. IEEE Trans. Vis. Comput. Graphics, 15(6):1391-1398, 2009.
    • (2009) IEEE Trans. Vis. Comput. Graphics , vol.15 , Issue.6 , pp. 1391-1398
    • Krone, M.1    Bidmon, K.2    Ertl, T.3
  • 34
    • 0028881975 scopus 로고
    • 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. J. Mol. Graphics, 13(5):323-330, 1995.
    • (1995) J. Mol. Graphics , vol.13 , Issue.5 , pp. 323-330
    • Laskowski, R.A.1
  • 36
    • 0027053611 scopus 로고
    • Pocket: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • D. G. Levitt and L. J. Banaszak. Pocket: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph., 10(4):229-234, 1992.
    • (1992) J. Mol. Graph. , vol.10 , Issue.4 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 37
    • 80855130019 scopus 로고    scopus 로고
    • Voronoi-based extraction and visualization of molecular paths
    • N. Lindow, D. Baum, and H.-C. Hege. Voronoi-based extraction and visualization of molecular paths. IEEE Trans. Vis. Comput. Graphics, 17(12):2025-2034, 2011.
    • (2011) IEEE Trans. Vis. Comput. Graphics , vol.17 , Issue.12 , pp. 2025-2034
    • Lindow, N.1    Baum, D.2    Hege, H.-C.3
  • 38
    • 77955729034 scopus 로고    scopus 로고
    • Accelerated visualization of dynamic molecular surfaces
    • N. Lindow, D. Baum, S. Prohaska, and H.-C. Hege. Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum, 29(3):943-952, 2010.
    • (2010) Comput. Graph. Forum , vol.29 , Issue.3 , pp. 943-952
    • Lindow, N.1    Baum, D.2    Prohaska, S.3    Hege, H.-C.4
  • 40
    • 0041784950 scopus 로고    scopus 로고
    • Allatom empirical potential for molecular modeling and dynamics studies of proteins
    • A. MacKerell, J. D. Bashford, M. Bellott, and R. Dunbrack et al. Allatom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102:3586-3616, 1998.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.1    Bashford, J.D.2    Bellott, M.3    Dunbrack, R.4
  • 41
    • 36449003554 scopus 로고
    • Constant-pressure molecular-dynamics algorithms
    • G. J. Martyna, D. J. Tobias, and M. L. Klein. Constant-pressure molecular-dynamics algorithms. J. Chem. Phys., 101:4177-4189, 1994.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 42
    • 84861407812 scopus 로고    scopus 로고
    • 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. J. of WSCG, 15(1-3):107-114, 2007.
    • (2007) J. of WSCG , vol.15 , Issue.1-3 , pp. 107-114
    • Medek, P.1    Beneš, P.2    Sochor, J.3
  • 43
    • 84872245502 scopus 로고    scopus 로고
    • MegaMol. http://vis-web.informatik.uni-stuttgart.de/trac/megamol.
    • MegaMol
  • 44
    • 0028835990 scopus 로고
    • Functional interactions in bacteriorhodopsin: A theoretical analysis of retinal hydrogen bonding with water
    • M. Nina, B. Roux, and J. Smith. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys. J., 68:25-39, 1995.
    • (1995) Biophys. J. , vol.68 , pp. 25-39
    • Nina, M.1    Roux, B.2    Smith, J.3
  • 45
    • 35748972048 scopus 로고    scopus 로고
    • MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
    • M. Petrěk, P. Kosinová, J. Koca, and M. Otyepka. 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
    • Petrěk, M.1    Kosinová, P.2    Koca, J.3    Otyepka, M.4
  • 46
    • 33847142225 scopus 로고    scopus 로고
    • CAVER: A new tool to explore routes from protein clefts, pockets and cavities
    • M. Petrěk, M. Otyepka, P. Banas, and P. Kosinová et al. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7(1):316+, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.1
    • Petrěk, M.1    Otyepka, M.2    Banas, P.3    Kosinová, P.4
  • 47
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • J. C. Phillips and K. Schulten et al. Scalable molecular dynamics with NAMD. J. Comput. Chem., 26:1781-1802, 2005.
    • (2005) J. Comput. Chem. , vol.26 , pp. 1781-1802
    • Phillips, J.C.1    Schulten, K.2
  • 48
    • 84872242804 scopus 로고    scopus 로고
    • PyMOL. http://pymol.org.
  • 49
    • 80855143291 scopus 로고    scopus 로고
    • dxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics
    • M. Raunest and C. Kandt. dxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics. J. Mol. Graph. Model., 2010.
    • (2010) J. Mol. Graph. Model.
    • Raunest, M.1    Kandt, C.2
  • 50
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • F. M. Richards. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bio., 6(1):151-176, 1977.
    • (1977) Annu. Rev. Biophys. Bio. , vol.6 , Issue.1 , pp. 151-176
    • Richards, F.M.1
  • 51
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of nalkanes
    • J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of nalkanes. J. Comput. Phys., 23:327-341, 1977.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 55
    • 0030404988 scopus 로고    scopus 로고
    • HOLE: A program for the analysis of the pore dimensions of ion channel structural models
    • O. S. Smart, J. G. Neduvelil, X.Wang, and B. A.Wallace et al. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph., 14(6), 1996.
    • (1996) J. Mol. Graph. , vol.14 , Issue.6
    • Smart, O.S.1    Neduvelil, J.G.2    Wang, X.3    Wallace, B.A.4
  • 56
    • 84882878737 scopus 로고    scopus 로고
    • Amira: A highly interactive system for visual data analysis
    • C. D. Hansen and C. R. Johnson, editors, Elsevier
    • D. Stalling, M. Westerhoff, and H.-C. Hege. Amira: A highly interactive system for visual data analysis. In C. D. Hansen and C. R. Johnson, editors, The Visualization Handbook, pages 749-767. Elsevier, 2005.
    • (2005) The Visualization Handbook , pp. 749-767
    • Stalling, D.1    Westerhoff, M.2    Hege, H.-C.3
  • 57
    • 0034128699 scopus 로고    scopus 로고
    • Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin
    • E. Tajkhorshid, J. Baudry, K. Schulten, and S. Suhai. Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Biophys. J., 78(2):683-693, 2000.
    • (2000) Biophys. J. , vol.78 , Issue.2 , pp. 683-693
    • Tajkhorshid, E.1    Baudry, J.2    Schulten, K.3    Suhai, S.4
  • 58
    • 77951214658 scopus 로고    scopus 로고
    • McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm
    • M. S. Till and M. Ullmann. McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J. Mol. Model., 16(3):419-429, 2010.
    • (2010) J. Mol. Model. , vol.16 , Issue.3 , pp. 419-429
    • Till, M.S.1    Ullmann, M.2
  • 59
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • M. Tuckerman and B. Berne. Reversible multiple time scale molecular dynamics. J. Chem. Phys., 97:1990-2001, 1992.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.2
  • 61
    • 84872240944 scopus 로고    scopus 로고
    • VMD
    • VMD. http://www.ks.uiuc.edu/Research/vmd.
  • 62
    • 77954262905 scopus 로고    scopus 로고
    • 3V: Cavity, channel and cleft volume calculator and extractor
    • N. R. Voss and M. Gerstein. 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res., 38(Suppl 2):W555-W562, 2010.
    • (2010) Nucleic Acids Res. , vol.38 , Issue.SUPPL. 2
    • Voss, N.R.1    Gerstein, M.2
  • 64
    • 75249088440 scopus 로고    scopus 로고
    • Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
    • J. Yu, Y. Zhou, I. Tanaka, and M. Yao. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, 26(1):46-52, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 46-52
    • Yu, J.1    Zhou, Y.2    Tanaka, I.3    Yao, M.4


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