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

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 comple...

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Bibliographic Details
Published inJournal of computer-aided molecular design Vol. 24; no. 5; pp. 417 - 422
Main Authors Seeliger, Daniel, de Groot, Bert L.
Format Journal Article
LanguageEnglish
Published Dordrecht Springer Netherlands 01.05.2010
Springer Nature B.V
Subjects
Affinity
Animal Anatomy
Binding
Binding Sites
Chemistry
Chemistry and Materials Science
Computer aided design
Computer Applications in Chemistry
Computer Graphics
Computer Simulation
Design engineering
Docking
Drug Design
Drugs
Histology
Ligands
Models, Molecular
Molecular Conformation
Morphology
Physical Chemistry
Software
Virtual reality
Autodock
Virtual screening
Docking
Vina
PyMOL
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Summary: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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ISSN:0920-654X
1573-4951
1573-4951
DOI:10.1007/s10822-010-9352-6