Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.

ABSTRACT: De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their comp

SUBMITTER: Allen WJ 

PROVIDER: S-EPMC5659719 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature