Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41.

ABSTRACT: Scoring functions are a critically important component of computer-aided screening methods for the identification of lead compounds during early stages of drug discovery. Here, we present a new multigrid implementation of the footprint similarity (FPS) scoring function that was recently developed in our laboratory which has proven useful for identification of compounds which bind to a protein on a per-residue basis in a way that resembles a known reference. The grid-based FPS method is much faster than its Cartesian-space counterpart, which makes it computationally tractable for on-the-fly docking, virtual screening, or de novo design. In this work, we establish that: (i) relatively few grids can be used to accurately approximate Cartesian space footprint similarity, (ii) the method yields

SUBMITTER: Balius TE 

PROVIDER: S-EPMC4016043 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature