Efficient molecular docking of NMR structures: application to HIV-1 protease.

ABSTRACT: Docking ligands into an ensemble of NMR conformers is essential to structure-based drug discovery if only NMR structures are available for the target. However, sequentially docking ligands into each NMR conformer through standard single-receptor-structure docking, referred to as sequential docking, is computationally expensive for large-scale database screening because of the large number of NMR conformers involved. Recently, we developed an efficient ensemble docking algorithm to consider protein structural variations in ligand binding. The algorithm simultaneously docks ligands into an ensemble of protein structures and achieves comparable performance to sequential docking without significant increase in computational time over single-structure docking. Here, we applied this algorithm to

SUBMITTER: Huang SY 

PROVIDER: S-EPMC2222846 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature