Preferred Interaction Patterns from Crystallographic Databases
A knowledge of three-dimensional structure, in all of its aspects, is an essential prerequisite of the molecular modelling process. This knowledge may be divided, on energetic grounds, into two categories. Firstly, information is required about the covalent aspects of three dimensional structure — bond lengths, valence angles, and conformational data which dictate the overall molecular shape. Secondly, geometrical descriptions are needed of the much weaker interactions by which atoms and molecules associate with each other in a non-bonded sense. Crystallography is unique in its ability to provide direct experimental results in both of these areas. The technique is now being applied to molecules of ever-increasing size and complexity and in ever-increasing numbers. Details of well over 100,000 crystal structures have been published — some 400 proteins and biological macromolecules, 76,000 small molecules containing organic carbon, and nearly 40,000 inorganic, mineral and metal structures: All of this information is of immense value and the advent of crystallographic databases makes the data more readily available in an organized form. It is now a relatively simple matter to locate relevant structures and extract their coordinates for use in modelling studies.
KeywordsBenzene Tyrosine Amide Glycine Cysteine
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- 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. Crystallogr., Sect. B; Struct. Sci. B35, 2331–2339.Google Scholar
- Allen, F. H., Bergerhoff, G., and Sievers, R. (1987a). Crystallographic Databases. Polycrystal Book Service, Dayton, Ohio.Google Scholar
- Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G., and Taylor, R. (1987b). Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc. Perkin Trans. II, S1–S19.Google Scholar
- Carson, M., and Hermans, J. (1985). Molecular dynamics workshop laboratory. In “Molecular Dynamics and Protein Structure” (J. Hermans,ed.), pp. 165–166. Polycrystal Book Service, Dayton, Ohio.Google Scholar
- Dunitz, J. (1979) X-ray Analysis and the Structure of Organic Molecules. Cornell University Press, Ithaca.Google Scholar
- Hamilton, W.C. and Ibers, J.A. (1968). Hydrogen Bonding in Solids. Benjamin,New York.Google Scholar
- Murray-Rust, P., and Motherwell, S. (1978). Computer retrieval and analysis of molecular geometry. III. Geometry of the 0–1’-aminofuranoside fragment. Acta. Crystallogr., Sect. B; Struct. Sci. B34, 2534–2546.Google Scholar
- Pauling, L. (1939). The Nature of the Chemical Bond. Cornell University Press, Ithaca.Google Scholar
- Pimentel, G.C. and McClellan, A.L. (1960). The Hydrogen Bond. Freeman, San Francisco.Google Scholar
- Schulz, G. E. and Schirmer, R. H. (1979). Principles of Protein Structure. Springer-Verlag, New York.Google Scholar