title: Avalanche for shape and feature-based virtual screening with 3D alignment.
abstract: This report introduces a new ligand-based virtual screening tool called Avalanche that incorporates both shape- and feature-based comparison with three-dimensional (3D) alignment between the query molecule and test compounds residing in a chemical database. Avalanche proceeds in two steps. The first step is an extremely rapid shape/feature based comparison which is used to narrow the focus from potentially millions or billions of candidate molecules and conformations to a more manageable number that are then passed to the second step. The second step is a detailed yet still rapid 3D alignment of the remaining candidate conformations to the query conformation. Using the 3D alignment, these remaining candidate conformations are scored, re-ranked and presented to the user as the top hits for further visualization and evaluation. To provide further insight into the method, the results from two prospective virtual screens are presented which show the ability of Avalanche to identify hits from chemical databases that would likely be missed by common substructure-based or fingerprint-based search methods. The Avalanche method is extended to enable patent landscaping, i.e., structural refinements to improve the patentability of hits for deployment in drug discovery campaigns.
authors.affiliation: Snowdon, Inc., Princeton, NJ, 08540, USA. djrdiller@gmail.com.|CMD Bioscience, 5 Science Park, New Haven, CT, 06511, USA. djrdiller@gmail.com.
authors.forename: David J
authors.initials: DJ
authors.lastname: Diller
authors.affiliation: Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
authors.forename: Nancy D
authors.initials: ND
authors.lastname: Connell
authors.affiliation: Department of Pharmacology, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, 08854, USA. welshwj@rwjms.rutgers.edu.
authors.forename: William J
authors.initials: WJ
authors.lastname: Welsh
mesh_terms: D055808:Drug Discovery; D008024:Ligands; D008968:Molecular Conformation; D015394:Molecular Structure; D054852:Small Molecule Libraries / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D054852:Small Molecule Libraries
keywords: Antibacterial drug discovery; Shape matching; Three dimensional alignment; Virtual screening