Flexible ligand docking using conformational ensembles

By D. Lorber, Brian K. Shoichet. 1998

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Molecular docking: a powerful approach for structure-based drug discovery. (2011, methodology): “For VS, 235,000 commercially available molecules were docked into the crystal structure of PTP-1B (PDB code 1pty) using the Northwestern University version [134-137] of DOCK3.”
Computational approaches streamlining drug discovery (2023, methodology): “The docking procedure itself can use molecular mechanics, often in internal coordinate representation, for rapid conformational sampling of fully flexible ligands 52,53 , using empirical 3D shape-matching approaches 54,55 , or combining them in a hybrid docking funnel 56,57 .”
Exploiting drug-disease relationships for computational drug repositioning (2011, unknown): “atomic and molecular interactions [31].”
Molecular docking and ligand specificity in fragment-based inhibitor discovery (2009, methodology): “Spheres were labeled for chemical matching based on the hydrogen bonding properties and ionization states of nearby protein atom”
Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity (1999, background): “However, when screening databases, DOCK typically keeps the ligands rigid, or docks a set of rigid conformers for each compound (Lorber & Shoichet 1998; Shoichet, Leach, & Kuntz 1999).”