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Volumn , Issue , 2010, Pages

Measuring properties of molecular surfaces using ray casting

Author keywords

Ray tracing; Surface area; Volume

Indexed keywords

GEOMETRIC PROPERTIES; INTERNAL CAVITIES; MOLECULAR SURFACES; RAY CASTING; SURFACE AREA;

EID: 77954077784     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPSW.2010.5470898     Document Type: Conference Paper
Times cited : (9)

References (40)
  • 2
    • 52049102653 scopus 로고    scopus 로고
    • Metamol: Highquality visualization of molecular skin surface
    • Sep, [Online]. Available
    • M. Chavent, B. Levy, and B. Maigret, "Metamol: highquality visualization of molecular skin surface." J Mol Graph Model, vol. 27, no. 2, pp. 209-216, Sep 2008. [Online]. Available: http://dx.doi.org/10.1016/j.jmgm. 2008.04.007.
    • (2008) J Mol Graph Model , vol.27 , Issue.2 , pp. 209-216
    • Chavent, M.1    Levy, B.2    Maigret, B.3
  • 3
    • 0032398742 scopus 로고    scopus 로고
    • Van der Waals surface graphs and molecular shape
    • D. Whitley, "Van der Waals surface graphs and molecular shape," J Math Chem, vol. 23, no. 3-4, pp. 377-397, 1998. (Pubitemid 128453263)
    • (1998) Journal of Mathematical Chemistry , vol.23 , Issue.3-4 , pp. 377-397
    • Whitley, D.C.1
  • 4
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Feb
    • B. Lee and F. M. Richards, "The interpretation of protein structures: estimation of static accessibility." J Mol Biol, vol. 55, no. 3, pp. 379-400, Feb 1971.
    • (1971) J Mol Biol , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 5
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • B. L. Greer, Jonathan Bush, "Macromolecular shape and surface maps by solvent exclusion," Biophysics, vol. 75, pp. 303-307, 1978.
    • (1978) Biophysics , vol.75 , pp. 303-307
    • Greer, B.L.1    Bush, J.2
  • 6
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • [Online]. Available
    • F. M. Richards, "Areas, volumes, packing and protein structure." Annu Rev Biophys Bioeng, vol. 6, pp. 151-176, 1977. [Online]. Available: http://dx.doi.org/10.1146/annurev.bb.06.060177.001055.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 7
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Aug
    • M. L. Connolly, "Solvent-accessible surfaces of proteins and nucleic acids." Science, vol. 221, no. 4612, pp. 709-713, Aug 1983.
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.L.1
  • 8
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Mar
    • M. F. Sanner, A. J. Olson, and J. C. Spehner, "Reduced surface: an efficient way to compute molecular surfaces." Biopolymers, vol. 38, no. 3, pp. 305-320, Mar 1996.
    • (1996) Biopolymers , vol.38 , Issue.3 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 9
    • 0027490298 scopus 로고
    • Molecular skins: A new concept for quantitative shape matching of a protein with its small molecule mimics
    • Oct, [Online]. Available
    • B. B. Masek, A. Merchant, and J. B. Matthew, "Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics." Proteins, vol. 17, no. 2, pp. 193-202, Oct 1993. [Online]. Available: http://dx.doi.org/10.1002/prot.340170208.
    • (1993) Proteins , vol.17 , Issue.2 , pp. 193-202
    • Masek, B.B.1    Merchant, A.2    Matthew, J.B.3
  • 11
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
    • Oct
    • J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, and S. Subramaniam, "Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape." Proteins, vol. 33, no. 1, pp. 1-17, Oct 1998.
    • (1998) Proteins , vol.33 , Issue.1 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 12
    • 36448970902 scopus 로고    scopus 로고
    • Molecular surfaces on proteins via beta shapes
    • J. Ryu, R. Park, and D.-S. Kim, "Molecular surfaces on proteins via beta shapes," Computer-Aided Design, vol. 39, pp. 1042-1057, 2007.
    • (2007) Computer-Aided Design , vol.39 , pp. 1042-1057
    • Ryu, J.1    Park, R.2    Kim, D.-S.3
  • 13
    • 38349095051 scopus 로고    scopus 로고
    • Minimal molecular surfaces and their applications
    • Feb, [Online]. Available
    • P. W. Bates, G. W. Wei, and S. Zhao, "Minimal molecular surfaces and their applications." J Comput Chem, vol. 29, no. 3, pp. 380-391, Feb 2008. [Online]. Available: http://dx.doi.org/10.1002/jcc.20796.
    • (2008) J Comput Chem , vol.29 , Issue.3 , pp. 380-391
    • Bates, P.W.1    Wei, G.W.2    Zhao, S.3
  • 14
    • 0000280208 scopus 로고
    • Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii
    • H. Gibson, K.D.; Scheraga, "Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii," Molecular Physics, vol. 62, p. 1247, 1987.
    • (1987) Molecular Physics , vol.62 , pp. 1247
    • Gibson, H.1    Scheraga, K.D.2
  • 15
    • 0021755764 scopus 로고
    • Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
    • Sep
    • T. J. Richmond, "Solvent accessible surface area and excluded volume in proteins. analytical equations for overlapping spheres and implications for the hydrophobic effect." J Mol Biol, vol. 178, no. 1, pp. 63-89, Sep 1984.
    • (1984) J Mol Biol , vol.178 , Issue.1 , pp. 63-89
    • Richmond, T.J.1
  • 16
    • 0037197254 scopus 로고    scopus 로고
    • Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
    • Apr, [Online]. Available
    • O. V. Tsodikov, M. T. Record, and Y. V. Sergeev, "Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature." J Comput Chem, vol. 23, no. 6, pp. 600-609, Apr 2002. [Online]. Available: http://dx.doi.org/10.1002/jcc.10061.
    • (2002) J Comput Chem , vol.23 , Issue.6 , pp. 600-609
    • Tsodikov, O.V.1    Record, M.T.2    Sergeev, Y.V.3
  • 17
    • 0001528720 scopus 로고    scopus 로고
    • Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
    • W. Fraczkiewicz, R. Braun, "Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules," Journal of Computational Chemistry, vol. 19, pp. 319-333, 1998.
    • (1998) Journal of Computational Chemistry , vol.19 , pp. 319-333
    • Fraczkiewicz, W.1    Braun, R.2
  • 18
    • 0029968922 scopus 로고    scopus 로고
    • The contour-buildup algorithm to calculate the analytical molecular surface
    • [Online]. Available
    • M. Totrov and R. Abagyan, "The contour-buildup algorithm to calculate the analytical molecular surface." J Struct Biol, vol. 116, no. 1, pp. 138-143, 1996. [Online]. Available: http://dx.doi.org/10.1006/jsbi.1996. 0022.
    • (1996) J Struct Biol , vol.116 , Issue.1 , pp. 138-143
    • Totrov, M.1    Abagyan, R.2
  • 19
    • 30344480798 scopus 로고    scopus 로고
    • Molecular surface generation using a variable-radius solvent probe
    • Jan, [Online]. Available
    • S. Bhat and E. O. Purisima, "Molecular surface generation using a variable-radius solvent probe." Proteins, vol. 62, no. 1, pp. 244-261, Jan 2006. [Online]. Available: http://dx.doi.org/10.1002/prot.20682.
    • (2006) Proteins , vol.62 , Issue.1 , pp. 244-261
    • Bhat, S.1    Purisima, E.O.2
  • 20
    • 0025487752 scopus 로고
    • Triangulation algorithms for the representation of molecular surface properties
    • Sep
    • W. Heiden, M. Schlenkrich, and J. Brickmann, "Triangulation algorithms for the representation of molecular surface properties." J Comput Aided Mol Des, vol. 4, no. 3, pp. 255-269, Sep 1990.
    • (1990) J Comput Aided Mol des , vol.4 , Issue.3 , pp. 255-269
    • Heiden, W.1    Schlenkrich, M.2    Brickmann, J.3
  • 21
    • 17044417175 scopus 로고    scopus 로고
    • Guaranteed quality triangulation of molecular skin surfaces
    • H.-L. Cheng and X. Shi, "Guaranteed quality triangulation of molecular skin surfaces," in IEEE Visualization, 2004.
    • (2004) IEEE Visualization
    • Cheng, H.-L.1    Shi, X.2
  • 23
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
    • Jan, [Online]. Available
    • W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig, "Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects." J Comput Chem, vol. 23, no. 1, pp. 128-137, Jan 2002. [Online]. Available: http://dx.doi.org/10.1002/jcc. 1161.
    • (2002) J Comput Chem , vol.23 , Issue.1 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 24
    • 84986431702 scopus 로고
    • On the analytical calculation of Van Der Waals surfaces and volumes: Some numerical aspects
    • M. Petitjean, "On the analytical calculation of van der waals surfaces and volumes: Some numerical aspects," Journal of Computational Chemistry, vol. 15, pp. 507-523, 1994.
    • (1994) Journal of Computational Chemistry , vol.15 , pp. 507-523
    • Petitjean, M.1
  • 26
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Jan
    • F. M. Richards, "The interpretation of protein structures: total volume, group volume distributions and packing density." J Mol Biol, vol. 82, no. 1, pp. 1-14, Jan 1974.
    • (1974) J Mol Biol , vol.82 , Issue.1 , pp. 1-14
    • Richards, F.M.1
  • 27
    • 0025492621 scopus 로고
    • Molecular volumes and surfaces of biomacromolecules via gepol: A fast and efficient algorithm
    • 151, Sep
    • E. Silla, F. Villar, O. Nilsson, J. L. Pascual-Ahuir, and O. Tapia, "Molecular volumes and surfaces of biomacromolecules via gepol: a fast and efficient algorithm." J Mol Graph, vol. 8, no. 3, pp. 168-72, 151, Sep 1990.
    • (1990) J Mol Graph , vol.8 , Issue.3 , pp. 168-172
    • Silla, E.1    Villar, F.2    Nilsson, O.3    Pascual-Ahuir, J.L.4    Tapia, O.5
  • 35
    • 52949132638 scopus 로고    scopus 로고
    • Cavities and atomic packing in protein structures and interfaces
    • 09
    • S. Sonavane and P. Chakrabarti, "Cavities and atomic packing in protein structures and interfaces," PLoS Comput Biol, vol. 4, no. 9, p. e1000188, 09 2008.
    • (2008) PLoS Comput Biol , vol.4 , Issue.9
    • Sonavane, S.1    Chakrabarti, P.2
  • 37
    • 0033665510 scopus 로고    scopus 로고
    • Ball - rapid software prototyping in computational molecular biology
    • [Online]. Available
    • O. Kohlbacher and H.-P. Lenhof, "Ball - rapid software prototyping in computational molecular biology," Bioinformatics, vol. 16, no. 9, p. 815824, 2000. [Online]. Available: http://www.ball-project.org.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 815824
    • Kohlbacher, O.1    Lenhof, H.-P.2
  • 39
    • 32144446593 scopus 로고    scopus 로고
    • Ballview: A tool for research and education in molecular modeling
    • [Online]. Available
    • A. Moll, A. Hildebrandt, H.-P. Lenhof, and O. Kohlbacher, "Ballview: a tool for research and education in molecular modeling." Bioinformatics, vol. 22, no. 3, pp. 365-366, 2006. [Online]. Available: http://dx.doi.org/10. 1093/bioinformatics/bti818.
    • (2006) Bioinformatics , vol.22 , Issue.3 , pp. 365-366
    • Moll, A.1    Hildebrandt, A.2    Lenhof, H.-P.3    Kohlbacher, O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.