|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 17.2, pp. 357-368
https://doi.org/10.1107/97809553602060000692 Chapter 17.2. Molecular graphics and animation
aThe Scripps Research Institute, La Jolla, CA 92037, USA |
References
Bailey, M., Schulten, K. & Johnson, J. (1998). The use of solid physical models for the study of macromolecular assembly. Curr. Opin. Struct. Biol. 8, 202–208.Google Scholar
Bajaj, C. L., Pascucci, V. & Schikore, D. R. (1996). Fast isocontouring for improved interactivity. In Proceedings of the ACM SIGGRAPH/IEEE symposium on volume visualization, pp. 39–46. San Francisco: ACM Press.Google Scholar
Barry, C. D. & McAlister, J. P. (1982). High performance molecular graphics, a hardware review. In Computational crystallography, edited by D. Sayre, pp. 274–255. Oxford: Clarendon Press.Google Scholar
Branden, C.-I., Jornvall, H., Eklund, H. & Fureugren, B. (1975). Alcohol dehydrogenase. In The enzymes, edited by P. Boyer, pp. 104–186. New York: Academic Press.Google Scholar
Brooks, J. P. Jr, Ouh-Young, M., Batter, J. J. & Kilpatrick, P. J. (1990). Project GROPE – haptic displays for scientific visualization. Comput. Graphics, 24, 177–186.Google Scholar
Burns, M. (1954). Automated fabrication: improving productivity in manufacturing. New Jersey: Prentice Hall.Google Scholar
Carson, M. (1991). RIBBONS 2.0. J. Appl. Cryst. 24, 958–961.Google Scholar
Connolly, M. L. (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709–713.Google Scholar
Connolly, M. L. & Olson, A. J. (1985). GRANNY, a companion to GRAMPS for the real-time manipulation of macromolecular models. Comput. Chem. 9, 1–6.Google Scholar
Diamond, R. (1982). BILDER: an interactive graphics program for biopolymers. In Computational crystallography, edited by D. Sayre, pp. 318–325. Oxford: Clarendon Press.Google Scholar
Drebein, R., Carpenter, L. & Hanrahan, P. (1988). Volume rendering. Proc. ACM SIGGRAPH'88 (Atlanta, Georgia, 1–5 August 1988). In Comput. Graphics Proc. Annu. Conf. Ser. 1988 (1993), pp. 65–74. New York: ACM SIGGRAPH.Google Scholar
Duncan, B. S. & Olson, A. J. (1993). Approximation and characterization of molecular surfaces. Biopolymers, 33, 219–229.Google Scholar
Duncan, B. S. & Olson, A. J. (1995). Approximation and visualization of large-scale motion of protein surfaces. J. Mol. Graphics, 13, 250–257.Google Scholar
Ferrin, T. E., Huang, C. C., Jarvis, L. E. & Langridge, R. (1988). The MIDAS display system. J. Mol. Graphics, 6, 13–27.Google Scholar
Goodford, P. J. (1985). A computational procedure for determining energetically favorable binding sites on biologically important molecules. J. Med. Chem. 28, 849–857.Google Scholar
Goodsell, D. S., Mian, I. S. & Olson, A. J. (1989). Rendering of volumetric data in molecular systems. J. Mol. Graphics, 7, 41–47.Google Scholar
Goodsell, D. S. & Olson, A. J. (1992). Molecular illustration in black and white. J. Mol. Graphics, 10, 235–240.Google Scholar
Gouraud, H. (1971). Continuous shading of curved surfaces. IEEE Trans. Comput. 20, 623–628.Google Scholar
Gwilliam, M. & Max, N. (1989). Atoms with shadows – an area-based algorithm for cast shadows on space-filling molecular models. J. Mol. Graphics, 7, 54–59.Google Scholar
Hessler, D. S., Young, S. J. & Ellisman, M. H. (1996). A flexible environment for visualization of three-dimensional biological structures. J. Struct. Biol. 116, 113–119.Google Scholar
Höhne, K. H., Bomans, M., Pommert, A., Reimer, M., Schiers, C., Tiede, U. & Wiebecke, G. (1989). 3D-visualization of tomographic volume data using the generalized voxel-model. Volume visualization workshop, Chapel Hill, NC. Department of Computer Science, University of North Carolina at Chapel Hill.Google Scholar
Hubbard, R. E. (1986). HYDRA: current and future developments. In Computer graphics and molecular modelling, edited by R. Fletterick & M. Zoller, pp. 9–12. Cold Spring Harbor Press.Google Scholar
Johnson, C. K. (1970). ORTEP: a Fortran thermal-ellipsoid plot program for crystal structure illustrations. Report ORNL 3794. Oak Ridge National Laboratory, Tennessee, USA.Google Scholar
Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Cryst. 11, 268–272.Google Scholar
Kabsch, W., Mannherz, H. G., Suck, D., Pai, E. F. & Holmes, K. C. (1990). Atomic structure of the actin/DNAse I complex. Nature (London), 347, 37–44.Google Scholar
Koradi, R., Billeter, M. & Wuthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics, 14, 51–55.Google Scholar
Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950.Google Scholar
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76.Google Scholar
Lauher, J. W. (1990). Chem-Ray: a molecular graphics program featuring an umbra and penumbra shadowing routine. J. Mol. Graphics, 8, 34–38.Google Scholar
Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.Google Scholar
Levinthal, C. (1966). Molecular modeling by computer. Sci. Am. 214, 42–52.Google Scholar
Lorenson, W. E. & Kline, H. E. (1987). Marching cubes: a high resolution 3D surface construction algorithm. Comput. Graphics, 21, 163–169.Google Scholar
Max, N. (1983). SIGGRAPH'84 call for OmniMax films. Comput. Graphics, 17, 73–76.Google Scholar
Motherwell, W. D. S. & Clegg, W. (1978). PLUTO. Program for plotting molecular and crystal structures. University of Cambridge, England.Google Scholar
Mujeeb, A., Kerwin, S. M., Kenyon, G. L. & James, T. L. (1993). Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra. Biochemistry, 32, 13419–13431.Google Scholar
Nichols, W. L., Rose, G. D., Ten Eyck, L. F. & Zimm, B. H. (1995). Rigid domains in proteins: an algorithmic approach to their identification. Proteins Struct. Funct. Genet. 23, 38–45.Google Scholar
O'Donnell, T. J. & Olson, A. J. (1981). GRAMPS – a graphics language interpreter for real-time, interactive three-dimensional picture editing and animation. Comput. Graphics, 15, 133–142.Google Scholar
Olson, A. J. (1981). Tomato bushy stunt virus. Film. Lawrence Berkeley Laboratory, University of California, Berkeley, California, USA.Google Scholar
Olson, A. J. (1983). Computer graphics in biomolecular science. NICOGRAPH '83, pp. 332–356. Tokyo: Nihon Keizai Shimbun, Inc.Google Scholar
Pepinsky, R. (1952). X-RAC and S-FAC: electronic analogue computers for X-ray analysis. In Computing methods and the phase problem in X-ray crystal analysis. Pennsylvania State College, USA.Google Scholar
Phillips, D. C. (1970). British biochemistry, past and present, edited by T. W. Goodwin, pp. 11–28. Academic Press.Google Scholar
Phong, B. T. (1975). Illumination for computer generated images. Commun. ACM, 18, 311–317.Google Scholar
Porter, T. K. (1979). The shaded surface display of large molecules. Comput. Graphics, 13, 234–236.Google Scholar
Ramachandran, G. N. & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283–437.Google Scholar
Richards, F. M. (1977). Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. A, 6, 151–176.Google Scholar
Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167–339.Google Scholar
Sanner, M.-F., Olson, A. J. & Spehner, J.-C. (1996). Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38, 305–320.Google Scholar
Sayle, R. A. & Milner-White, E. J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374.Google Scholar
Taylor, R. M. I., Robinett, W., Chi, V. L., Brooks, F. P. Jr, Wright, W. V., Williams, R. S. & Snyder, E. J. (1993). The nanomanipulator: a virtual reality interface for a scanning tunnelling microscope. Proc. ACM SIGGRAPH'93 (Anaheim, California, 1–6 August 1993). In Comput. Graphics Proc. Annu. Conf. Ser. 1993 (1993), pp. 127–133. New York: ACM SIGGRAPH.Google Scholar
Teschner, M., Henn, C., Vollhardt, H., Reiling, S. & Brinkmann, J. (1994). Texture mapping: a new tool for molecular graphics. J. Mol. Graphics, 12, 98–105.Google Scholar
Wright, W. V. (1982). GRIP – an interactive computer graphics system for molecular studies. In Computational crystallography, edited by D. Sayre, pp. 294–302. Oxford: Clarendon Press. Google Scholar