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Fast 3D shape screening of large chemical databases through alignment-recycling

Methodology     Fast 3D shape screening of large chemical databases through alignment-recycling Fabien Fontaine, Evan E Bolton, Yulia Borodina, Stephen H Bryant Chemistry Central Journal 2007, 1:12 (6 June 2007) [Abstract] [Provisional PDF]

A new method for efficiently performing 3D structural searches in a dataset of more than one million PubChem compounds of limited size (<28 heavy atoms) and flexibility (<6 rotatable bonds) is presented. In current 3D search methods, it is necessary to compute the optimal overlay between the query and database molecules to obtain shape similarity values, a necessity that adds a significant amount of overhead to the search time. The alignment-recycling method presented in this article, however, reduces the CPU time required to perform shape similarity searches. The authors also discuss extensions and variations to the methodology, for example, to handle more flexible and larger small-molecules. The article will interest those who are working in the field of 3D molecular alignment and related disciplines.

Posted by Gino D'Oca at 14:02    Comments (0)