Ligand docking and binding site analysis with PyMOL and Autodock/Vina

By Daniel Seeliger, B. L. de Groot. 2010

2,389 citations recorded by the source corpus.

Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and interactions are mandatory. Here we present an interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina and demonstrate how the combination of docking and visualization can aid structure-based drug design efforts.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

Molecular dynamics simulations and novel drug discovery (2018, background): “docking poses are scored, and the compounds are ranked according to the score [113,114].”
Computer-aided drug design platform using PyMOL (2011, methodology): “Recently, Seeliger et al. [ 11 ] have published a PyMOL plugin for AutoDock and AutoDock Vina.”
Using PyMOL as a platform for computational drug design (2017, methodology): “The Autodock/ Vina 41 plugin enables users to perform various tasks including de ﬁ ning binding sites and exporting to Autodock and VINA input ﬁ les, performing receptor and ligand preparation automatically, executing docking with Autodock or VINA, visualizing grid maps generated by autogrid in PyMO”