Chapter 3.3. Molecular modelling and graphics

References

Abad-Zapatero, C., Abdel-Meguid, S. S., Johnson, J. E., Leslie, A. G. W., Rayment, I., Rossmann, M. G., Suck, D. & Tsukihara, T. (1980). Structure of southern bean mosaic virus at 2.8 Å resolution. Nature (London), 286, 33–39.Google Scholar
Abi-Ezzi, S. S. & Bunshaft, A. J. (1986). An implementer's view of PHIGS. IEEE Comput. Graphics Appl. Vol. 6, Part 2.Google Scholar
Aharonov, Y., Farach, H. A. & Poole, C. P. (1977). Non-linear vector product to describe rotations. Am. J. Phys. 45, 451–454.Google Scholar
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Cryst. B35, 2331–2339.Google Scholar
Allinger, N. L. (1976). Calculation of molecular structure and energy by force field methods. Adv. Phys. Org. Chem. 13, 1–82.Google Scholar
Altona, C. & Sundaralingam, M. (1972). Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94(23), 8205–8212.Google Scholar
American National Standards Institute, American National Standard for Information Processing Systems – Computer Graphics – Graphical Kernel System (GKS) Functional Description (1985). ISO 7942, ISO Central Secretariat, Geneva, Switzerland.Google Scholar
American National Standards Institute, American National Standard for Information Processing Systems – Computer Graphics – Programmer's Hierarchical Graphics System (PHIGS) Functional Description, Archive File Format, Clear-Text Encoding of Archive File (1988). ANSI X3.144–1988. ANSI, New York, USA.Google Scholar
Anderson, S. (1984). Graphical representation of molecules and substructure-search queries in MACCS. J. Mol. Graphics, 2, 83–90.Google Scholar
Arnold, D. B. & Bono, P. R. (1988). CGM and CGI: metafile and interface standards for computer graphics. Berlin: Springer-Verlag.Google Scholar
Barry, C. D. & North, A. C. T. (1971). The use of a computer-controlled display system in the study of molecular conformations. Cold Spring Harbour Symp. Quant. Biol. 36, 577–584.Google Scholar
Bash, P. A., Pattabiraman, N., Huang, C., Ferrin, T. E. & Langridge, R. (1983). Van der Waals surfaces in molecular modelling: implementation with real-time computer graphics. Science, 222, 1325–1327.Google Scholar
Beddell, C. J. (1970). An X-ray crystallographic study of the activity of lysozyme. DPhil thesis, University of Oxford, England.Google Scholar
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar
Bloomer, A. C., Champness, J. N., Bricogne, G., Staden, R. & Klug, A. (1978). Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within and between subunits. Nature (London), 276, 362–368.Google Scholar
Boyd, D. B. & Lipkowitz, K. B. (1982). Molecular mechanics, the method and its underlying philosophy. J. Chem. Educ. 59, 269–274.Google Scholar
Brandenburg, N. P., Dempsey, S., Dijkstra, B. W., Lijk, L. J. & Hol, W. G. J. (1981). An interactive graphics system for comparing and model building of macromolecules. J. Appl. Cryst. 14, 274–279.Google Scholar
Brooks, B. R., Brucolleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187–217.Google Scholar
Brown, M. D. (1985). Understanding PHIGS. Template, Megatek Corp., San Diego, California, USA.Google Scholar
Burkert, U. & Allinger, N. L. (1982). Molecular mechanics. ACS Monogr. No. 177.Google Scholar
Cambillau, C. & Horjales, E. (1987). TOM: a FRODO subpackage for protein-ligand fitting with interactive energy minimization. J. Mol. Graphics, 5, 174–177.Google Scholar
Cambillau, C., Horjales, E. & Jones, T. A. (1984). TOM, a display program for fitting ligands into protein receptors and performing interactive energy minimization. J. Mol. Graphics, 2, 53–54.Google Scholar
Cambridge Structural Database (1994). Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, England.Google Scholar
Cockrell, P. R. (1983). A new general purpose method for large volume production of contour charts. Comput. Graphics Forum, 2, 35–47.Google Scholar
Cohen, N. C. (1971). GEMO: a computer program for the calculation of the preferred conformations of organic molecules. Tetrahedron, 27, 789–797.Google Scholar
Cohen, N. C., Colin, P. & Lemoine, G. (1981). Script: interactive molecular geometrical treatments on the basis of computer-drawn chemical formula. Tetrahedron, 37, 1711–1721.Google Scholar
Collins, D. M., Cotton, F. A., Hazen, E. E., Meyer, E. F. & Morimoto, C. N. (1975). Protein crystal structures: quicker, cheaper approaches. Science, 190, 1047–1053.Google Scholar
Connolly, M. L. (1983a). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709–713.Google Scholar
Connolly, M. L. (1983b). Analytical molecular surface calculation. J. Appl. Cryst. 16, 548–558.Google Scholar
Dam, A. van (1988). PHIGS+ functional description, revision 3.0. Comput. Graphics, 22, 125–218.Google Scholar
Dayringer, H. E., Tramontano, A., Sprang, S. R. & Fletterick, R. J. (1986). Interactive program for visualization and modelling of proteins, nucleic acids and small molecules. J. Mol. Graphics, 4, 82–87.Google Scholar
Diamond, R. (1966). A mathematical model-building procedure for proteins. Acta Cryst. 21, 253–266.Google Scholar
Diamond, R. (1971). A real-space refinement procedure for proteins. Acta Cryst. A27, 436–452.Google Scholar
Diamond, R. (1976a). On the comparison of conformations using linear and quadratic transformations. Acta Cryst. A32, 1–10.Google Scholar
Diamond, R. (1976b). Model building techniques for macromolecules. In Crystallographic computing techniques, edited by F. R. Ahmed, K. Huml & B. Sedlacek, pp. 336–343. Copenhagen: Munksgaard.Google Scholar
Diamond, R. (1980a). BILDER: a computer graphics program for biopolymers and its application to the interpretation of the structure of tobacco mosaic virus protein discs at 2.8 Å resolution. In Biomolecular structure, conformation, function and evolution, Vol. 1, edited by R. Srinivasan, pp. 567–588. Oxford: Pergamon Press.Google Scholar
Diamond, R. (1980b). Some problems in macromolecular map interpretation. In Computing in crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 21.01–21.19. Bangalore: Indian Academy of Sciences for the International Union of Crystallography.Google Scholar
Diamond, R. (1980c). Inter-active graphics. In Computing in crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 27.01–27.16. Bangalore: Indian Academy of Sciences for the International Union of Crystallography.Google Scholar
Diamond, R. (1981). A review of the principles and properties of the method of least squares. In Structural aspects of biomolecules, edited by R. Srinivasan & V. Pattabhi, pp. 81–122. Delhi: Macmillan India Ltd.Google Scholar
Diamond, R. (1982a). Two contouring algorithms. In Computational crystallography, edited by D. Sayre, pp. 266–272. Oxford University Press.Google Scholar
Diamond, R. (1982b). BILDER: an interactive graphics program for biopolymers. In Computational crystallography, edited by D. Sayre, pp. 318–325. Oxford University Press.Google Scholar
Diamond, R. (1984a). Applications of computer graphics in molecular biology. Comput. Graphics Forum, 3, 3–11.Google Scholar
Diamond, R. (1984b). Least squares and related optimisation techniques. In Methods and applications in crystallographic computing, edited by S. R. Hall & T. Ashida, pp. 174–192. Oxford University Press.Google Scholar
Diamond, R. (1988). A note on the rotational superposition problem. Acta Cryst. A44, 211–216.Google Scholar
Diamond, R. (1989). A comparison of three recently published methods for superimposing vector sets by pure rotation. Acta Cryst. A45, 657.Google Scholar
Diamond, R. (1990a). On the factorisation of rotations with special reference to diffractometry. Proc. R. Soc. London Ser. A, 428, 451–472.Google Scholar
Diamond, R. (1990b). Chirality in rotational superposition. Acta Cryst. A46, 423.Google Scholar
Diamond, R., Wynn, A., Thomsen, K. & Turner, J. (1982). Three-dimensional perception for one-eyed guys, or, the use of dynamic parallax. In Computational crystallography, edited by D. Sayre, pp. 286–293. Oxford University Press.Google Scholar
Dodson, E. J., Isaacs, N. W. & Rollett, J. S. (1976). A method for fitting satisfactory models to sets of atomic positions in protein structure refinements. Acta Cryst. A32, 311–315.Google Scholar
Dodson, G. G., Eliopoulos, E. E., Isaacs, N. W., McCall, M. J., Niall, H. D. & North, A. C. T. (1982). Rat relaxin: insulin-like fold predicts a likely receptor binding region. Int. J. Biol. Macromol. 4, 399–405.Google Scholar
Enderle, G., Kansy, K. & Pfaff, G. (1984). Computer graphics programming, GKS – the graphics standard. Berlin: Springer-Verlag.Google Scholar
Evans, P. R., Farrants, G. W. & Hudson, P. J. (1981). Phosphofructokinase: structure and control. Philos. Trans. R. Soc. London Ser. B, 293, 53–62.Google Scholar
Feldmann, R. J. (1976). The design of computing systems for molecular modeling. Annu. Rev. Biophys. Bioeng. 5, 477–510.Google Scholar
Feldmann, R. J. (1983). Directions in macromolecular structure representation and display. In Computer applications in chemistry, edited by S. R. Heller & R. Potenzone Jr, pp. 9–18. Amsterdam: Elsevier.Google Scholar
Feldmann, R. J., Bing, D. H., Furie, B. C. & Furie, B. (1978). Interactive computer surface graphics approach to the study of the active site of bovine trypsin. Proc. Natl Acad. Sci. Biochemistry, 75, 5409–5412.Google Scholar
Ferrin, T. E., Huang, C., Jarvis, L. & Langridge, R. (1984). Molecular inter-active display and simulation: MIDAS. J. Mol. Graphics, 2, 55.Google Scholar
Foley, J. D., van Dam, A., Feiner, S. K. & Hughes, J. F. (1990). Computer graphics principles and practice, 2nd edition. New York: Addison Wesley.Google Scholar
Ford, L. O., Johnson, L. N., Machin, P. A., Phillips, D. C. & Tjian, R. (1974). Crystal structure of a lysozyme-tetrasaccharide lactone complex. J. Mol. Biol. 88, 349–371.Google Scholar
Gallo, L., Huang, C. & Ferrin, T. (1983). UCSF MIDAS, molecular interactive display and simulation, users' guide. Computer Graphics Laboratory, School of Pharmacy, University of California, San Francisco, USA.Google Scholar
Gill, P. E., Murray, W. & Wright, M. H. (1981). Practical optimization. Orlando, Florida: Academic Press.Google Scholar
Gilliland, G. L. & Quiocho, F. A. (1981). Structure of the L-arabinose-binding protein from Escherichia coli at 2.4 Å resolution. J. Mol. Biol. 146, 341–362.Google Scholar
Girling, R. L., Houston, T. E., Schmidt, W. C. Jr & Amma, E. L. (1980). Macromolecular structure refinement by restrained least-squares and interactive graphics as applied to sickling deer type III hemoglobin. Acta Cryst. A36, 43–50.Google Scholar
Gossling, T. H. (1967). Two methods of presentation of electron-density maps using a small-store computer. Acta Cryst. 22, 465–468.Google Scholar
Greer, J. (1974). Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins. J. Mol. Biol. 82, 279–302.Google Scholar
Harris, M. R., Geddes, A. J. & North, A. C. T. (1985). A liquid crystal stereo-viewer for molecular graphics. J. Mol. Graphics, 3, 121–122.Google Scholar
Hass, B. S., Willoughby, T. V., Morimoto, C. N., Cullen, D. L. & Meyer, E. F. (1975). The solution of the structure of spirodienone by visual packing analysis. Acta Cryst. B31, 1225–1229.Google Scholar
Heap, B. R. & Pink, M. G. (1969). Three contouring algorithms, DNAM Rep. 81. National Physical Laboratory, Teddington, England.Google Scholar
Hermans, J. (1985). Rationalization of molecular models. In Methods in enzymology, Vol. 115. Diffraction methods for biological molecules, Part B, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 171–189. Orlando, Florida: Academic Press.Google Scholar
Hermans, J. & McQueen, J. E. (1974). Computer manipulation of (macro) molecules with the method of local change. Acta Cryst. A30, 730–739.Google Scholar
Hogle, J., Rao, S. T., Mallikarjunan, M., Beddell, C., McMullan, R. K. & Sundaralingam, M. (1981). Studies of monoclinic hen egg white lysozyme. Structure solution at 4 Å resolution and molecular-packing comparisons with tetragonal and triclinic lysozymes. Acta Cryst. B37, 591–597.Google Scholar
Hopgood, F. R. A., Duce, D. A., Gallop, J. R. & Sutcliffe, D. C. (1986). Introduction to the graphical kernel system, 2nd ed. London: Academic Press.Google Scholar
Hubbard, R. E. (1983). Colour molecular graphics on a microcomputer. J. Mol. Graphics, 1, 13–16, C3–C4.Google Scholar
Hubbard, R. E. (1985). The representation of protein structure. In Computer aided molecular design, pp. 99–106. Proceedings of a two-day conference, London, October 1984. London: Oyez Scientific.Google Scholar
International Standards Organisation, International Standard Information Processing Systems – Computer Graphics – Graphical Kernel System for Three Dimensions (GKS-3D), Functional Description (1988). ISO Document No. 8805:1988(E). American National Standards Institute, New York, USA.Google Scholar
International Tables for Crystallography (2005). Vol. A. Space-group symmetry, edited by T. Hahn. Heidelberg: Springer.Google Scholar
IUPAC–IUB Commission on Biochemical Nomenclature (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. J. Biol. Chem. 245, 6489–6497.Google Scholar
Johnson, C. K. (1970). Drawing crystal structures by computer. In Crystallographic computing, edited by F. R. Ahmed, pp. 227–230. Copenhagen: Munksgaard.Google Scholar
Johnson, C. K. (1976). ORTEPII. A Fortran thermal-ellipsoid plot program for crystal structure illustrations. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.Google Scholar
Johnson, C. K. (1980). Computer-generated illustrations. In Computing in crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 26.01–26.10. Bangalore: Indian Academy of Sciences for the International Union of Crystallography.Google Scholar
Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Cryst. 11, 268–272.Google Scholar
Jones, T. A. (1982). FRODO: a graphics fitting program for macromolecules. In Computational crystallography, edited by D. Sayre, pp. 303–317. Oxford University Press.Google Scholar
Jones, T. A. (1985). Interactive computer graphics: FRODO. In Methods in enzymology, Vol. 115. Diffraction methods for biological molecules, Part B, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 157–171. Orlando, Florida: Academic Press.Google Scholar
Jones, T. A. & Liljas, L. (1984). Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Cryst. A40, 50–57.Google Scholar
Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.Google Scholar
Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Cryst. A32, 922–923.Google Scholar
Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst. A34, 827–828.Google Scholar
Katz, L. & Levinthal, C. (1972). Interactive computer graphics and representation of complex biological structures. Annu. Rev. Biophys. Bioeng. 1, 465–504.Google Scholar
Kearsley, S. K. (1989). On the orthogonal transformation used for structural comparisons. Acta Cryst. A45, 208–210.Google Scholar
Langridge, R., Ferrin, T. E., Kuntz, I. D. & Connolly, M. L. (1981). Real-time color graphics in studies of molecular interactions. Science, 211, 661–666.Google Scholar
Lederer, F., Glatigny, A., Bethge, P. H., Bellamy, H. D. & Mathews, F. S. (1981). Improvement of the 2.5 Å resolution model of cytochrome b₅₆₂ by re-determining the primary structure and using molecular graphics. J. Mol. Biol. 148, 427–448.Google Scholar
Lesk, A. M. & Hardman, K. D. (1982). Computer-generated schematic diagrams of protein structures. Science, 216, 539–540.Google Scholar
Lesk, A. M. & Hardman, K. D. (1985). Computer-generated pictures of proteins. In Methods in enzymology, Vol. 115. Diffraction methods for biological molecules, Part B, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 381–390. Orlando, Florida: Academic Press.Google Scholar
Levinthal, C. (1966). Molecular model-building by computer. Sci. Am. 214, 42–52.Google Scholar
Levitt, M. (1971). PhD Dissertation, ch. 2. University of Cambridge, England.Google Scholar
Levitt, M. (1974). Energy refinement of hen egg-white lysozyme. J. Mol. Biol. 82, 393–420.Google Scholar
Levitt, M. & Lifson, S. (1969). Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol. 46, 269–279.Google Scholar
Levitt, M. & Warshel, A. (1975). Computer simulation of protein folding. Nature (London), 253, 694–698.Google Scholar
Lieth, C. W. van der, Carter, R. E., Dolata, D. P. & Liljefors, T. (1984). RINGS – a general program to build ring systems. J. Mol. Graphics, 2, 117–123.Google Scholar
Liljefors, T. (1983). MOLBUILD – an interactive computer graphics interface to molecular mechanics. J. Mol. Graphics, 1, 111–117.Google Scholar
Luenberger, D. G. (1984). Linear and nonlinear programming. Reading, Massachusetts: Addison Wesley.Google Scholar
Mackay, A. L. (1984). Quaternion transformation of molecular orientation. Acta Cryst. A40, 165–166.Google Scholar
McLachlan, A. D. (1972). A mathematical procedure for superimposing atomic coordinates of proteins. Acta Cryst. A28, 656–657.Google Scholar
McLachlan, A. D. (1979). Gene duplications in the structural evolution of chymotrypsin. Appendix: Least squares fitting of two structures. J. Mol. Biol. 128, 49–79.Google Scholar
McLachlan, A. D. (1982). Rapid comparison of protein structures. Acta Cryst. A38, 871–873.Google Scholar
Max, N. L. (1984). Computer representation of molecular surfaces. J. Mol. Graphics, 2, 8–13, C2–C4.Google Scholar
Meyer, E. F. (1970). Three-dimensional graphical models of molecules and a time-slicing computer. J. Appl. Cryst. 3, 392–395.Google Scholar
Meyer, E. F. (1971). Interactive computer display for the three dimensional study of macromolecular structures. Nature (London), 232, 255–257.Google Scholar
Meyer, E. F. (1974). Storage and retrieval of macromolecular structural data. Biopolymers, 13, 419–422.Google Scholar
Miller, J. R., Abdel-Meguid, S. S., Rossmann, M. G. & Anderson, D. C. (1981). A computer graphics system for the building of macromolecular models into electron density maps. J. Appl. Cryst. 14, 94–100.Google Scholar
Morffew, A. J. (1983). Bibliography for molecular graphics. J. Mol. Graphics, 1, 17–23.Google Scholar
Morffew, A. J. (1984). Bibliography for molecular graphics, 1983/84. J. Mol. Graphics, 2, 124–128.Google Scholar
Morimoto, C. N. & Meyer, E. F. (1976). Information retrieval, computer graphics, and remote computing. In Crystallographic computing techniques, edited by F. R. Ahmed, K. Huml & B. Sedlacek, pp. 488–496. Copenhagen: Munksgaard.Google Scholar
Motherwell, W. D. S. (1978). Pluto – a program for displaying molecular and crystal structures. Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, England.Google Scholar
Newman, W. M. & Sproull, R. F. (1973). Principles of inter-active computer graphics. New York: McGraw-Hill.Google Scholar
North, A. C. T. (1982). Use of interactive computer graphics in studying molecular structures and interactions. Chem. Ind. pp. 221–225.Google Scholar
North, A. C. T., Denson, A. K., Evans, A. C., Ford, L. O. & Willoughby, T. V. (1981). The use of an interactive computer graphics system in the study of protein conformations. In Biomolecular structure, conformation, function and evolution, Vol. 1, edited by R. Srinivasan, pp. 59–72. Oxford: Pergamon Press.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. (1982). GRAMPS: a high level graphics interpreter for expanding graphics utilization. In Computational crystallography, edited by D. Sayre, pp. 326–336. Oxford University Press.Google Scholar
Opdenbosch, N. van, Cramer, R. III & Giarrusso, F. F. (1985). Sybyl, the integrated molecular modelling system. J. Mol. Graphics, 3, 110–111.Google Scholar
Pearl, L. H. & Honegger, A. (1983). Generation of molecular surfaces for graphic display. J. Mol. Graphics, 1, 9–12, C2.Google Scholar
Phillips, S. E. V. (1980). Structure and refinement of oxymyoglobin at 1.6 Å resolution. J. Mol. Biol. 142, 531–554.Google Scholar
Phong, B. T. (1975). Illumination for computer generated images. Commun. ACM, 18, 311–317.Google Scholar
Porter, T. K. (1978). Spherical shading. Comput. Graphics, 12, 282–285.Google Scholar
Potenzone, R., Cavicchi, E., Weintraub, H. J. R. & Hopfinger, A. J. (1977). Molecular mechanics and the CAMSEQ processor. Comput. Chem. 1, 187–194.Google Scholar
Potterton, E. A., Geddes, A. J. & North, A. C. T. (1983). Attempts to design inhibitors of dihydrofolate reductase using interactive computer graphics with real time energy calculations. In Chemistry and biology of pteridines, edited by J. A. Blair, pp. 299–303. Berlin, New York: Walter de Gruyter.Google Scholar
Purisima, E. O. & Scheraga, H. A. (1986). An approach to the multiple-minima problem by relaxing dimensionality. Proc. Natl Acad. Sci. USA, 83, 2782–2786.Google Scholar
Richardson, J. S. (1977). β-Sheet topology and the relatedness of proteins. Nature (London), 268, 495–500.Google Scholar
Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167–339.Google Scholar
Richardson, J. S. (1985). Schematic drawings of protein structures. In Methods in enzymology, Vol. 115. Diffraction methods for biological molecules, Part B, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 359–380. Orlando, Florida: Academic Press.Google Scholar
Sundaram, K. & Radhakrishnan, R. (1979). A computer program for topographic analysis of biomolecular systems. Comput. Programs Biomed. 10, 34–42.Google Scholar
Sutcliffe, D. C. (1980). Contouring over rectangular and skewed rectangular grids – an introduction. In Mathematical methods in computer graphics and design, edited by K. W. Brodie, pp. 39–62. London: Academic Press.Google Scholar
Sutherland, I. E., Sproull, R. F. & Schumacker, R. A. (1974). A characterization of ten hidden surface algorithms. Comput. Surv. 6, 1–55.Google Scholar
Swanson, S. M., Wesolowski, T., Geller, M. & Meyer, E. F. (1989). Animation: a useful tool for protein molecular dynamicists, applied to hydrogen bonds in the active site of elastase. J. Mol. Graphics, 7, 240–242, 223–224.Google Scholar
Takenaka, A. & Sasada, Y. (1980). Computer manipulation of crystal and molecular models. J. Crystallogr. Soc. Jpn, 22, 214–225. [In Japanese.]Google Scholar
Thomas, D. J. (1993). Toward more reliable printed stereo. J. Mol. Graphics, 11, 15–22.Google Scholar
Tsernoglou, D., Petsko, G. A., McQueen, J. E. & Hermans, J. (1977). Molecular graphics: application to the structure determination of a snake venom neurotoxin. Science, 197, 1378–1381.Google Scholar
Vedani, A. & Meyer, E. F. (1984). Structure–activity relationships of sulfonamide drugs and human carbonic anhydrase C: modelling of inhibitor molecules into receptor site of the enzyme with an interactive computer graphics display. J. Pharm. Sci. 73, 352–358.Google Scholar
Walsh, G. R. (1975). Methods of optimization. London: John Wiley.Google Scholar
Warme, P. K., Go, N. & Scheraga, H. A. (1972). Refinement of X-ray data of proteins. 1. Adjustment of atomic coordinates to conform to a specified geometry. J. Comput. Phys. 9, 303–317.Google Scholar
Williams, T. V. (1982). Thesis. University of North Carolina at Chapel Hill, NC, USA.Google Scholar
Willoughby, T. V., Morimoto, C. N., Sparks, R. A. & Meyer, E. F. (1974). Mini-computer control of a stereo graphics display. J. Appl. Cryst. 7, 430–434.Google Scholar
Wipke, W. T. (1974). Computer assisted three-dimensional synthetic analysis. In Computer representation and manipulation of chemical information, edited by W. T. Wipke, S. R. Heller, R. J. Feldmann & E. Hyde, pp. 147–174. New York: John Wiley.Google Scholar
Wipke, W. T., Braun, H., Smith, G., Choplin, F. & Sieber, W. (1977). SECS – simulation and evaluation of chemical synthesis: strategy and planning. ACS Symp. Ser. 61, 97–125.Google Scholar
Wipke, W. T. & Dyott, T. M. (1974). Simulation and evaluation of chemical synthesis. Computer representation and manipulation of stereochemistry. J. Am. Chem. Soc. 96, 4825–4834.Google Scholar