Skip to main content

Abstract

Structure databanks contain atomic coordinates, bibliographic citations, and other information related to structural studies. Numeric structural data for organics, organometallics and metal complexes studied by X-ray and neutron diffraction are available from the Cambridge Crystallographic Data Centre (CCDC) and from other similar databanks worldwide (Allen et al., 1979, Allen et. al., 1987). This and the Inorganic Crystal Structure Database (CRYSTIN) in Karlsruhe, for example, may become essential for studying interactions of drugs with macromolecules or the coordination of ligands in metalloproteins. The Protein Data Bank (PDB) at Brookhaven National Laboratory (Bernstein et al, 1977) was established in 1971 as a computer-based system of three-dimensional structures of biological macromolecules and is used mainly to study protein structure and modelling (Koetzle et al., 1989). There are also a NRC Metals Crystallographic Data File (CRYSTMET) which contains 23,000 metallic phases, a Powder Diffraction File, and a U.S. National Bureau of Standards Crystal Data File (CRYSTDAT) which contains data on all crystalline solids for which the basic cell parameters are known: this amounts to about 130,000 compounds (Abola et al., 1988).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abola E.E., Bernstein F.C., and Koetzle T.F., 1988, The Protein Data Bank, 69–81 in Lesk A.M., (Ed.), Computational molecular biology: sources and methods for sequence analysis, Oxford University Press, Oxford.

    Google Scholar 

  • Allen F., 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., and Watson D.G., 1979, “The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information,” Acta Cryst., B35, 2331–2339.

    CAS  Google Scholar 

  • Allen F.H., Bergerhoff G., and Stevens R., (Eds.) 1987, Crystallographic databases, International Union of Crystallography, Chester, U.K.

    Google Scholar 

  • Askigg D., Bleasby A.J., Dix N.I.M., Findlay J.B.C., North A.C.I., Parry-Smith D., Wootton J.C., Blundell T.L., Gardner S.P., Hayes F., Haslam S., Sternberg M.J.E., Thornton J.M., Tickle I.J., 1988, “A protein sequence/structure database”, Nature, 335, 20 October, 745–748.

    Article  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., and Tasumi M., 1977, “The Protein Data Bank: a computer-based archival file for macromolecular structures”, J. Molec. Biol., 122, 535–542.

    Article  Google Scholar 

  • Brint A.T., Davies H.M., Mitchell E.M., and Willett P., 1989, “Rapid geometric searching in protein structures”, J.Mol.Graphics, 7, 48–53.

    Article  CAS  Google Scholar 

  • C.B.M.I.U.C., 1989, “Policy on publication and the deposition of data from crystallographic studies of biological macromolecules. The Commission on Biological Macromolecules of the International Union of Crystallography Report, International Union of Crystallography”, Acta Cryst., B45, 518–519.

    Google Scholar 

  • Doubet S., Bock K., Smith D., Darvill A., and Albersheim P., 1989, “The comple carbohydrate structure database”, Trends in Biochemical Sciences, 14, December, 475–477.

    Article  PubMed  CAS  Google Scholar 

  • Jansson P.-E., Kenne L., and Widmalm G., 1989, “Computer-assisted structural analysis of polysaccarides with an extended version of CASPER using 1H and 13C-n.m.r. data”, Carbohydrate Research, 188, 169–191.

    Article  PubMed  CAS  Google Scholar 

  • Koetzle T.F., Abola E.E., Bernstein F.C., Bryant S.H., and Weng J., 1989, Collection and standardisation of crystal structure data by the Protein Data Bank 77–81 in Colewell R.R., Biomolecular data: a resource in transition, Oxford University Press, Oxford.

    Google Scholar 

  • Lesk A.M., 1989, Integrated access to sequence and structural data: principles of design of comprehensive databases for molecular biology, 189–198 in Colewell R.R., Biomolecular data: a resource in transition, Oxford University Press, Oxford.

    Google Scholar 

  • Mitchell M., Artymiuk P.J., Rice D.W., and Willett P., 1990, “Use of techniques derived from graph theory to compare secondary motifs in proteins”, J. Mol. Biol., 212, 151–166.

    Article  PubMed  CAS  Google Scholar 

  • Protein Data Bank, 1985, Atomic coordinates and bibliographic entry format description, Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973, U.S.A.

    Google Scholar 

  • Thornton J.M., and Gardner S.P., 1989, “Protein motifs and database searching”, Trends. Biochem.Sci. 14, 300–304.

    Article  PubMed  CAS  Google Scholar 

  • U.S.D.O.E., 1986, Summary report of a workshop on a carbohydrate structure database held at Auburn, New York, August 7–9, U.S. Department of Energy, Division of Biological Energy Research, Washington D.C., DOE/ER-0310.

    Google Scholar 

  • Wlodawer A., Savage H., and Dodson G., 1989, “Structure of insulin: results of joint neutron and X-ray refinement”, Acta Cryst., B45, 99–107.

    CAS  Google Scholar 

  • Wood G.H., Rodgers J.R., and Gough S.R., 1989, “Canadian scientific numeric database service”, J. Chem. Inf. Comput. Sci., 29, 118–123.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 1991 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Sillince, J.A.A., Sillince, M. (1991). The Main Structure Databanks in Molecular Science. In: Molecular Databases for Protein Sequences and Structure Studies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-76809-5_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-76809-5_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-76811-8

  • Online ISBN: 978-3-642-76809-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics