Virtual Screening with AutoDock: Theory and Practice

By Sandro Cosconati, Stefano Forli, A. Perryman, Rodney Harris, David S. Goodsell, Arthur J. Olson. Expert Opinion on Drug Discovery, 2010

643 citations recorded by the source corpus.

Importance of the field: Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review: We describe virtual screening methods that are available in the AutoDock suite of programs and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain: A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message: Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dea6177a415820b543da0a81d366dff93d7e8684

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Citations in the corpus

Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, neutral): “Because large-scale virtual screens that involve docking are often constrained by computational requirements, compound libraries are typically filtered to remove redundancy while at the same time maximizing the diversity within the dataset (186, 187).”
Computational protein-ligand docking and virtual drug screening with the AutoDock suite (2016, methodology): “The default methods used in AutoDock and AutoDock Vina are highly effective for typical drug-like ligands, and they have been widely used for applications such as virtual screening 25 .”
The design and development of covalent protein-protein interaction inhibitors for cancer treatment (2020, background): “The flexibility of side chains is another important factor to consider for covalent docking [76].”
Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls (2015, background): “The most common docking programs and software include Autodock [31], Autodock Vina [32], GOLD [33] and FlexX [34].”