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

2010/04/16 by Daniel Seeliger, Bert L. de Groot · 15 citations
Computer Science · Biochemistry, Genetics and Molecular Biology · Materials Science · #Computational Drug Discovery Methods #Protein Structure and Dynamics #Enzyme Structure and Function

paper · pdf · doi:10.1007/s10822-010-9352-6

Abstract

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.

Citations

• Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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