Ligand docking and binding site analysis with PyMOL and Autodock/Vina |
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Authors: | Daniel Seeliger Bert L de Groot |
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Institution: | (1) Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany |
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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. |
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