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A hierarchical method for generating low-energy conformers of a protein-ligand complex

✍ Scribed by James A. Given; Michael K. Gilson

Publisher
John Wiley and Sons
Year
1998
Tongue
English
Weight
304 KB
Volume
33
Category
Article
ISSN
0887-3585

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✦ Synopsis

A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented.

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