Automated docking of flexible ligands: Applications of autodock

Abstract

AutoDock is a suite of C programs used to predict the bound conformations of a small, flexible ligand to a macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation. This paper reviews recent applications of the technique and describes the enhancements included in the current release.

Molecular docking of balanol to dynamics snapshots of protein kinase A

“…Table I also includes results for several modified balanol models in which different partial charges were turned off. The calculated binding energy between balanol and PKA is similar to that obtained from a previous continuum electrostatics calculation28 although the electrostatics contributions are somewhat larger in the Autodock20, 21 model. The docking experiments recovered the original structure quite well for every run in every snapshot with an overall root‐mean‐square structural difference of only 0.27 Å.…”

Identification of a Novel Binding Site Between HIV Type 1 Nef C-Terminal Flexible Loop and AP2 Required for Nef-Mediated CD4 Downregulation

“…First, the S 163 LLHPM 168 segment of the Nef loop (including the L 164 L 165 dileucine motif) was docked into the crystal structure of AP2 25 using the AutoDock program. 27 The top scoring docking solutions confirmed that the Nef dileucine motif binds into the previously identified dileucine motif binding pocket in AP2 25 (Fig. 3, orange patch).…”

Molecular Mechanics Force Fields and their Applications in Drug Design

“…The scoring function in the first docking program DOCK [169,170] uses the AMBER force field [75] specifically adapted to estimate the binding affinity of molecules. Similarly AutoDock [171] which is also used to predict the bound conformation of a small flexible ligand to a macromolecular target of known structure also utilizes the second-generation AMBER force field for scoring.…”