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Original Articles

Visualizing The Future of Molecular Graphics

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Pages 233-247 | Received 02 Feb 1997, Accepted 17 May 1997, Published online: 05 Oct 2006

References

  • Barry , C. D. 1982 . “ High performance molecular graphics, a hardware review ” . In Computational Crystallography , Edited by: Sayer , D. 274 – 285 . Oxford : Clarendon Press .
  • Brooks , F. P. , Ouh-Young , M. , Batter , J. J. and Kilpartrick , J. P. 1990 . Project GROPE – haptic displays for scientific visualization . Comput. Graphics , 24 : 177 – 185 .
  • Colloc'h , N. and Mornon , J.-P. 1990 . A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighbourhood . J. Mol. Graphics , 8 : 133 – 140 .
  • Connolly , M. L. 1983 . Solvent-accessible surfaces of proteins and nucleic acids . Science , 221 : 709 – 713 .
  • Connolly , M. L. and Olson , A. J. 1985 . GRANNY, a companion to GRAMPS for the real-time manipulation of macromolecular models . Comput. Chem. , 9 : 1 – 6 .
  • Diamond , R. 1982 . “ BILDER: an interactive graphics program for biopolymers ” . In Computational Crystallography , Edited by: Sayer , D. 318 – 325 . Oxford : Clarendon Press .
  • Duncan , B. S. and Olson , A. J. 1993 . Approximation and characterization of molecular surfaces . Biopolymers , 33 : 219 – 229 .
  • Duncan , B. S. and Olson , A. J. 1995a . Approximation and visualization of large-scale motion of protein surfaces . J. Mol. Graphics , 13 : 250 – 257 .
  • Duncan , B. S. and Olson , A. J. 1995b . Texture mapping parametric molecular surfaces . J. Mol. Graphics , 13 : 258 – 264 .
  • Ferrin , T. E. , Huang , C. C. , Jarvis , L. E. and Langridge , R. 1988 . The MIDAS display system . J. Mol. Graphics , 6 : 13 – 27 .
  • Fisher , C. L. , Tainer , J. A. , Pique , M. E. and Getzoff , E. D. 1990 . Visualization of molecular flexibility and its effects on electrostatic recognition . J. Mol. Graphics , 8 : 125 – 132 .
  • Goodford , P. J. 1985 . A computational procedure for determined energetically favorable binding sites on biologically important molecules . J. Med. Chem. , 28 : 849 – 857 .
  • Goodsell , D. S. , Mian , I. S. and Olson , A. J. 1989 . Rendering volumetric data in molecular systems . J. Mol. Graphics , 7 : 41 – 47 .
  • Gosling , J. and McGilton , H. 1995, 1995 . The Java Language Environment. Sun Microsystems White Paper , May
  • Johnson , C. K. 1970 . “ ORTEP: A Fortran thermal-ellipsoid plot program for crystal structure illustrations ” . Oak Ridge National Laboratory Report, ORNL-3794: 1970 . (abstract)
  • Jones , T. A. 1978 . FRODO: a graphics model building and refinement system for macromolecules . J. Appl. Crystallogr. , 11 : 268 – 272 .
  • Hubbard , R. E. 1986 . “ HYDRA: Current and future developments ” . In Computer Graphics and Molecular Modelling , Edited by: Fletterick , R. and Zoller , M. 9 – 12 . Cold Spring Harbor, Cold Spring Harbor Press .
  • Klein , T. E. , Huang , C. C. , Petterson , E. F. , Cough , G. S. , Ferrin , T. E. and Langridge , R. 1990 . A real-time malleable molecular surface . J. Mol. Graphics , 8 : 16 – 24 .
  • Koendrick , J. J. 1990 . Solid Shape , Cambridge : MIT Press .
  • Kuntz , I. D. , Blaney , J. M. , Oatley , S. , Langridge , R. and Ferrin , T. 1982 . A geometric approach to macromolecule-ligand interactions . J. Mol. Biol. , 161 : 269 – 288 .
  • Lee , B. and Richards , F. M. 1971 . The interpretation of protein structures: estimation of static accessibility . J. Mol. Biol. , 55 : 379 – 400 .
  • Leicester , S. E. , Finney , J. L. and Bywater , R. P. 1988 . Description of moleculer surface shape using Fourier descriptors . J. Mol. Graphics , 6 : 104 – 108 .
  • Levinthal , C. 1965 . Molecular modeling by computer . Sci. Am. , 214 : 42 – 52 .
  • Martin , C. H. , Chen , Z. P. and Birge , R. R. 1997 . “ Towards a bacteriorhodopsin-silicon neuromorphic photosensor ” . In Pacific Symposium on Biocomputing 1997 , Edited by: Altman , R. B. , Dunker , K. B. and Klein , T. E. 268 – 280 . Singapore : World Scientific Press .
  • Max , N. L. and Getzoff , E. D. 1988 . Spherical harmonic molecular surfaces . IEEE Computer Graphics Appl. , 8 : 40 – 42 .
  • Naughton , P. 1996 . The Java Handbook , Osborne : McGraw Hill .
  • O'Donnell , T. J. and Olson , A. J. 1981 . GRAMPS – A graphics language interpreter for real-time, interactive three-dimensional picture editing and animation . Comput. Graphics , 15 : 133 – 142 .
  • Olson , A. J. and Goodsell , D. S. 1991 . “ A functional view of proteins ” . In Visualization Blackboard , Edited by: Rosenblum , L. J. 15 – 17 . IEEE .
  • Palmer , T. C. 1992 . Software and system design . J. Mol. Graphics , 10 : 42 – 43 .
  • Parge , H. E. , Forest , K. T. , Hickey , M. J. , Christiansen , D. A. , Getzoff , E. D. and Tainer , J. A. 1995 . Structure of fibre-forming protin pilin at 2.6 Å resolution . Nature , 378 : 32 – 38 .
  • Pique , M. 1996 . Prototype Molecular Viewer in Java . Prototype Molecular Viewer In Java , URL http://www.sdsc.edu/CCMS: NSF Computational Center for Macromolecular Structure
  • Potts , D. B. M. , Smith , J. , Akke , M. , Macke , T. J. , Okazaki , K. , Hidaka , H. , Case , D. A. and Chazin , W. J. 1995 . The three-dimensional structure of calcyclin reveals a novel homodimeric motif for S100 calcium binding proteins . Nature Struct. Biol. , 2 : 790 – 799 .
  • Richards , F. M. 1977 . Areas, volumes, packing and protein structure . Ann. Rev. Biophys. Bioeng. , 6 : 151 – 176 .
  • Richardson , J. S. 1981 . The anatomy and taxonomy of protein structure . Adv. Prot. Chem. , 34 : 167 – 339 .
  • Sanner , M. , Widmer , A. , Senn , H. and Braun , W. 1989 . GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data . J. Comput. Aided Mol. Des. , 3 : 195 – 210 .
  • Sanner , M. F. and Olson , A. J. 1997 . “ Real time surface reconstruction for moving molecular fragments ” . In Pacific Symposium on Biocomputing 1997 , Edited by: Altman , R. B. , Dunker , K. B. and Klein , T. E. 385 – 396 . Singapore : World Scientific Press .
  • Sanner , M. F. , Olson , A. J. and Spehner , J. C. 1996 . Reduced surface: an efficient way to compute molecular surfaces . Biopolymers , 38 : 305 – 320 .
  • Strynadka , N. C. J. , Eisenstein , M. , Katchalski-Katsir , E. , Shoichet , B. K. , Kuntz , I. D. , Abagyan , R. , Totrov , M. , Hanin , J. , Cherfils , J. , Zimmerman , F. , Olson , A. , Duncan , B. , Rao , M. , Jackson , R. , Sternberg , M. and James , M. N. G. 1996 . Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase . Nature Struct. Biol. , 3 : 233 – 239 .
  • Surles , M. D. 1992 . An algorithm with linear complexity for interactive, physically-based modeling of large proteins . Comput. Graphics , 26 : 221 – 230 .
  • Taylor , R. M. II , Robinett , W. , Chi , V. L. , Brooks , F. P. Jr. , Wright , W. V. , Williams , R. S. and Snyder , E. J. The nanomanipulator: A virtual reality interface for a scanning tunnelling microscope . Computer Graphics Annual Conference Series, SIGGRAPH Conference Proceedings . 1–6 August 1993 . pp. 127 – 134 . ACM SIGGRAPH .
  • Techsner , M. , Henn , C. , Vollhardt , H. , Reiling , S. and Brinkmann , J. 1994 . Texture mapping: A new tool for molecular graphics . J. Mol. Graphics , 12 : 98 – 105 .
  • Tuffrey , P. , Vaney , M. C. , Mornon , J. P. and Hazout , S. 1991 . FORME: an interactive package for protein backbone deformation . J. Mol. Graphics , 9 : 175 – 181 .
  • Upson , C. , Faulhaber , T. Jr. , Kamins , D. , Laidlaw , D. , Schlegel , D. , Vroom , J. , Gurwitz , R. and van Dam , A. 1989 . The application visualization system: A computational environment for scientific visualization . IEEE Comput. Graphics Appl. , 9 : 30 – 42 .
  • Wright , W. V. 1982 . “ GRIP: an interactive computer graphics system for molecular studies ” . In Computational Crystallography , Edited by: Sayer , D. 294 – 302 . Oxford : Clarendon Press .

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