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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Published in	Journal of computer-aided molecular design Vol. 24; no. 5; pp. 417 - 422
Main Authors	Seeliger, Daniel, de Groot, Bert L.
Format	Journal Article
Language	English
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
Online Access	Get full text
ISSN	0920-654X 1573-4951 1573-4951
DOI	10.1007/s10822-010-9352-6

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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.
AbstractList	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. 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.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. 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.[PUBLICATION ABSTRACT]
Author	Seeliger, Daniel de Groot, Bert L.
Author_xml	– sequence: 1 givenname: Daniel surname: Seeliger fullname: Seeliger, Daniel email: dseelig@gwdg.de organization: Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry – sequence: 2 givenname: Bert L. surname: de Groot fullname: de Groot, Bert L. organization: Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/20401516$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B 10.1073/pnas.181342398 10.1186/1471-2105-9-126 10.1002/jcc.20634 10.1002/pro.5560070905 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O 10.1016/j.tibs.2007.03.008 10.1186/1471-2105-7-316 10.1093/bioinformatics/btl197 10.1002/biot.200600208 10.1038/nrd1549 10.1002/jcc.21334
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Snippet	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...
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SubjectTerms	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
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Title	Ligand docking and binding site analysis with PyMOL and Autodock/Vina
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