𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Functionality maps of binding sites: A multiple copy simultaneous search method

✍ Scribed by Dr. Andrew Miranker; Martin Karplus

Book ID
105358581
Publisher
John Wiley and Sons
Year
1991
Tongue
English
Weight
832 KB
Volume
11
Category
Article
ISSN
0887-3585

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✦ Synopsis

Abstract

A new method is proposed for determining energetically favorable positions and orientations for functional groups on the surface of proteins with known three‐dimensional structure. From 1,000 to 5,000 copies of a functional group are randomly placed in the site and subjected to simultaneous energy minimization and/or quenched molecular dynamics. The resulting functionality maps of a protein receptor site, which can take account of its flexibility, can be used for the analysis of protein ligand interactions and rational drug design. Application of the method to the sialic acid binding site of the influenza coat protein, hemagglutinin, yields functional group minima that correspond with those of the ligand in a cocrystal structure.

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