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

ABSTRACT:

Background

Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.

Results

Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matri

SUBMITTER: Fontaine F 

PROVIDER: S-EPMC1994057 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature