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  • Title: Evaluation of docking strategies for virtual screening of compound databases: cAMP-dependent serine/threonine kinase as an example.
    Author: Godden JW, Stahura F, Bajorath J.
    Journal: J Mol Graph Model; 1998 Jun; 16(3):139-43, 165. PubMed ID: 10434253.
    Abstract:
    In an effort to establish efficient docking routines for computational screening of compound databases on protein structures, cAMP-dependent protein kinase has been selected as a test case and a variety of docking options and scoring functions were compared. These included rigid-body and flexible docking and scoring based on surface complementarity and/or force field energy. Inhibitors were removed from complex crystal structures and added to compound libraries in their binding conformations and, in addition, deliberately modified conformations. Rigid-body docking and contact scoring well reproduced two of three experimental enzyme-inhibitor complexes. Ligand docking with flexible torsional angles failed to do so but anchored search of some inhibitors converged near to experimental structures, however, only when energy scoring was applied.
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