International
Tables for
Crystallography
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2006). Vol. B, ch. 3.3, p. 384   | 1 | 2 |

Section 3.3.3.2.10. O

R. Diamonda*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: rd10@cam.ac.uk

3.3.3.2.10. O

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Jones et al. (1991[link]) have developed a modelling system for proteins with a radically different approach to any of the foregoing, in that they begin by reducing the available electron-density map to a skeletal representation (Greer, 1974[link]; Williams, 1982[link]) which consists of a line running through the density close to its maximal values, this being the basis of a chain trace. Provisional α-carbon positions are also estimated at this stage. A database of known structures is then scanned for pentapeptides which may be superimposed on five successive positions in the chain trace, the best fit so found being taken to provide coordinates for the three central residues of the developing model. The process advances by three residues at each step, the first and last residues of the pentapeptide being used only to ensure that the central residues are built in a manner compatible with what precedes and follows.

The process ensures that conformations so built are free from improbable conformations, and the whole forms an adequate starting structure for molecular-dynamics procedures, even though some imperfect geometry is to be expected where each tripeptide joins the next.

References

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
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
Williams, T. V. (1982). Thesis. University of North Carolina at Chapel Hill, NC, USA.Google Scholar








































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