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7 - Docking: a domesday report

from PART II - COMPUTATIONAL CHEMISTRY METHODOLOGY

Published online by Cambridge University Press:  06 July 2010

By
Martha S. Head
Edited by
Kenneth M. Merz, Jr ,
Dagmar Ringe  and
Charles H. Reynolds
Kenneth M. Merz, Jr
Affiliation:
University of Florida
Dagmar Ringe
Affiliation:
Brandeis University, Massachusetts
Charles H. Reynolds
Affiliation:
Johnson & Johnson Pharmaceutical Research & Development
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Summary

In 1085, most likely from a desire to audit his tax revenues, William the Conqueror commissioned a survey of the land and resources of the country over which he reigned. The results of that survey come down to us in two tomes, the Little Domesday and the Great Domesday, in which were recorded voluminous amounts of data concerning the land, people, buildings, and chattel throughout England. By no means was this a complete record; large swathes of urban England – London, for example – were not included, nor was there any census of church personnel or property. The Little and Great Domesday books accordingly are an odd mix of completeness and incompleteness, leaving out such large parts of English society yet cataloguing to an excruciating level of detail within the areas surveyed.

Similarly, this chapter is a complete yet incomplete survey of the docking and scoring landscape. We do not review the general principles of docking technologies; a sufficient number of such reviews have been published in peer-reviewed journals alone. Nor do we evaluate the state of the art for docking programs and scoring functions; a number of well-regarded and careful evaluations describe the current capabilities and limitations of the technology. Instead, under “Comments on the Theory of Docking” we will make explicit the connections between docking and a theory of noncovalent association.

Type
Chapter
Information
Drug Design
Structure- and Ligand-Based Approaches
 , pp. 98 - 119
Publisher: Cambridge University Press
Print publication year: 2010

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