| Ligand docking and binding site analysis with PyMOL and Autodock/Vina. | |
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MedLine Citation:
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PMID: 20401516 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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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Authors:
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Daniel Seeliger; Bert L de Groot |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-04-17 |
Journal Detail:
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Title: Journal of computer-aided molecular design Volume: 24 ISSN: 1573-4951 ISO Abbreviation: J. Comput. Aided Mol. Des. Publication Date: 2010 May |
Date Detail:
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Created Date: 2010-06-07 Completed Date: 2010-09-03 Revised Date: 2010-09-30 |
Medline Journal Info:
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Nlm Unique ID: 8710425 Medline TA: J Comput Aided Mol Des Country: Netherlands |
Other Details:
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Languages: eng Pagination: 417-22 Citation Subset: IM |
Affiliation:
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Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. dseelig@gwdg.de |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Binding Sites Computer Graphics* Computer Simulation* Drug Design Ligands Models, Molecular* Molecular Conformation Software |
| Chemical | |
Reg. No./Substance:
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0/Ligands |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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