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Volumn 27, Issue 2, 2008, Pages 209-216

MetaMol: High-quality visualization of molecular skin surface

Author keywords

GPU; Mixed complex; Molecular skin surface; Ray casting; Smooth molecular surface

Indexed keywords

BIOINFORMATICS; CHEMICAL PROPERTIES; CHLORINE COMPOUNDS; COMMUNICATION CHANNELS (INFORMATION THEORY); SKIN; SURFACE CHEMISTRY;

EID: 52049102653     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.04.007     Document Type: Article
Times cited : (34)

References (38)
  • 1
    • 52049119089 scopus 로고    scopus 로고
    • Molecular surfaces: calculations, uses and representations
    • Chapman M., and Connolly M.L. Molecular surfaces: calculations, uses and representations. Int. Tables Crystallogr. (2001) 539-545
    • (2001) Int. Tables Crystallogr. , pp. 539-545
    • Chapman, M.1    Connolly, M.L.2
  • 2
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 3
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards F.M. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6 (1977) 151-176
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 4
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • Greer J., and Bush B.L. Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. U.S.A. 75 (1978) 303-307
    • (1978) Proc. Natl. Acad. Sci. U.S.A. , vol.75 , pp. 303-307
    • Greer, J.1    Bush, B.L.2
  • 5
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly M.L. Analytical molecular surface calculation. J. Appl. Crystallogr. 16 (1983) 548-558
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 6
    • 0033482642 scopus 로고    scopus 로고
    • Deformable smooth surface design
    • Edelsbrunner H. Deformable smooth surface design. Discrete Comput. Geom. 21 (1999) 87-115
    • (1999) Discrete Comput. Geom. , vol.21 , pp. 87-115
    • Edelsbrunner, H.1
  • 7
    • 0001309005 scopus 로고
    • Molecular surface triangulation
    • Connolly M.L. Molecular surface triangulation. J. Appl. Crystallogr. 18 (1985) 499-505
    • (1985) J. Appl. Crystallogr. , vol.18 , pp. 499-505
    • Connolly, M.L.1
  • 8
    • 0028514996 scopus 로고    scopus 로고
    • A. Varshney, F.P.J. Brooks, W.V. Wright, Linearly scalable computation of smooth molecular, surfaces, IEEE Comput. Graph. Appl., 14 (1994) 19-25.
    • A. Varshney, F.P.J. Brooks, W.V. Wright, Linearly scalable computation of smooth molecular, surfaces, IEEE Comput. Graph. Appl., 14 (1994) 19-25.
  • 9
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: an efficient way to compute molecular surfaces
    • Sanner M.F., Olson A.J., and Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38 (1996) 305-320
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 10
    • 33750517742 scopus 로고    scopus 로고
    • Efficient molecular surface generation using level-set methods
    • Can T., Chen C.-I., and Wang Y.-F. Efficient molecular surface generation using level-set methods. J. Mol. Graph. Model. 25 (2006) 442-454
    • (2006) J. Mol. Graph. Model. , vol.25 , pp. 442-454
    • Can, T.1    Chen, C.-I.2    Wang, Y.-F.3
  • 11
    • 44849127123 scopus 로고    scopus 로고
    • Minimal molecular surfaces and their applications
    • Bates P.W., Wei G.W., and Zhao S. Minimal molecular surfaces and their applications. J. Comput. Chem. (2007)
    • (2007) J. Comput. Chem.
    • Bates, P.W.1    Wei, G.W.2    Zhao, S.3
  • 12
    • 2942736986 scopus 로고    scopus 로고
    • Approximation by skin surfaces
    • Kruithof N., and Vegter G. Approximation by skin surfaces. Comput-Aid. Des. 36 (2004) 1075-1088
    • (2004) Comput-Aid. Des. , vol.36 , pp. 1075-1088
    • Kruithof, N.1    Vegter, G.2
  • 13
    • 17044417175 scopus 로고    scopus 로고
    • Guaranteed quality triangulation of molecular skin surfaces
    • IEEE Computer Society
    • Cheng H.-L., and Shi X. Guaranteed quality triangulation of molecular skin surfaces. Proceedings of the Conference on Visualization '04. IEEE Computer Society (2004) 481-488
    • (2004) Proceedings of the Conference on Visualization '04 , pp. 481-488
    • Cheng, H.-L.1    Shi, X.2
  • 14
    • 33749438758 scopus 로고    scopus 로고
    • H.-L. Cheng, X. Shi, Quality mesh generation for molecular skin surfaces using restricted union of balls, IEEE Visualization, 2005, 399-405.
    • H.-L. Cheng, X. Shi, Quality mesh generation for molecular skin surfaces using restricted union of balls, IEEE Visualization, 2005, 399-405.
  • 15
    • 52049096208 scopus 로고    scopus 로고
    • R. Toledo, B. Levy, Extending the graphic pipeline with new GPU-accelerated primitives, Tech report, 2004.
    • R. Toledo, B. Levy, Extending the graphic pipeline with new GPU-accelerated primitives, Tech report, 2004.
  • 19
    • 52049114953 scopus 로고    scopus 로고
    • Cgal, Computational Geometry Algorithms Library, 1999, http://www.cgal.org.
    • Cgal, Computational Geometry Algorithms Library, 1999, http://www.cgal.org.
  • 20
    • 33749235307 scopus 로고    scopus 로고
    • Real-time GPU rendering of piecewise algebraic surfaces
    • Loop C., and Blinn J. Real-time GPU rendering of piecewise algebraic surfaces. ACM Trans. Graph. 25 (2006) 664-670
    • (2006) ACM Trans. Graph. , vol.25 , pp. 664-670
    • Loop, C.1    Blinn, J.2
  • 22
    • 0030793507 scopus 로고    scopus 로고
    • SIMS: computation of a smooth invariant molecular surface
    • Vorobjev Y.N., and Hermans J. SIMS: computation of a smooth invariant molecular surface. Biophys. J. 73 (1997) 722-732
    • (1997) Biophys. J. , vol.73 , pp. 722-732
    • Vorobjev, Y.N.1    Hermans, J.2
  • 23
    • 34648817162 scopus 로고    scopus 로고
    • Treatment of charge singularities in implicit solvent models
    • 114106 pp.
    • Geng W., Yu S., and Wei G. Treatment of charge singularities in implicit solvent models. J. Chem. Phys. 127 (2007) 114106 pp.
    • (2007) J. Chem. Phys. , vol.127
    • Geng, W.1    Yu, S.2    Wei, G.3
  • 25
    • 84867972679 scopus 로고    scopus 로고
    • Meshing skin surfaces with certified topology
    • Kruithof N., and Vegter G. Meshing skin surfaces with certified topology. Comput. Geom. Theor. Appl. 36 (2007) 166-182
    • (2007) Comput. Geom. Theor. Appl. , vol.36 , pp. 166-182
    • Kruithof, N.1    Vegter, G.2
  • 28
    • 0000720929 scopus 로고    scopus 로고
    • Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
    • Ritchie D.W., and Kemp G.J.L. Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J. Comput. Chem. 20 (1999) 383-395
    • (1999) J. Comput. Chem. , vol.20 , pp. 383-395
    • Ritchie, D.W.1    Kemp, G.J.L.2
  • 29
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 281-299
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 31
    • 52049124592 scopus 로고    scopus 로고
    • X. Hao, A. Varshney, S. Sukharev, Real-time visualization of large time-varying molecules, in: Proceedings of the High-Performance Computing Symposium '04, (2004) 109-114.
    • X. Hao, A. Varshney, S. Sukharev, Real-time visualization of large time-varying molecules, in: Proceedings of the High-Performance Computing Symposium '04, (2004) 109-114.
  • 33
    • 0031300887 scopus 로고    scopus 로고
    • Real time surface reconstruction for moving molecular fragments
    • Sanner M.F., and Olson A.J. Real time surface reconstruction for moving molecular fragments. Pac. Symp. Biocomput. (1997) 385-396
    • (1997) Pac. Symp. Biocomput. , pp. 385-396
    • Sanner, M.F.1    Olson, A.J.2
  • 37
    • 33845621535 scopus 로고    scopus 로고
    • Ambient occlusion and edge cueing for enhancing real time molecular visualization
    • Tarini M., Cignoni P., and Montani C. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans. Vis. Comput. Graph. 12 (2006) 1237-1244
    • (2006) IEEE Trans. Vis. Comput. Graph. , vol.12 , pp. 1237-1244
    • Tarini, M.1    Cignoni, P.2    Montani, C.3
  • 38
    • 52049125289 scopus 로고    scopus 로고
    • E. Krieger, YASARA, 2003, www.yasara.org.
    • E. Krieger, YASARA, 2003, www.yasara.org.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.