Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called “pathway docking” in which molecular docking was used to screen ligand-receptor binding free ener...

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Bibliographic Details
Published in:Journal of computer-aided molecular design 2013-08, Vol.27 (8), p.689-695
Main Authors: Tran, Diem-Trang T., Le, Ly T., Truong, Thanh N.
Format: Article
Language:English
Subjects:
Animal Anatomy
Animals
Antiviral Agents - pharmacology
Avian flu
Binding sites
Birds
CAD
Chemistry
Chemistry and Materials Science
Computer aided design
Computer Applications in Chemistry
Enzyme Inhibitors - pharmacology
Enzymes
Histology
Influenza A virus
Influenza A Virus, H5N1 Subtype - drug effects
Influenza A Virus, H5N1 Subtype - enzymology
Influenza in Birds - drug therapy
Influenza in Birds - enzymology
Influenza in Birds - virology
Molecular Docking Simulation - economics
Molecular structure
Morphology
Neuraminidase - metabolism
Oseltamivir - pharmacology
Pharmaceutical sciences
Physical Chemistry
Protein Binding
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Summary:Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called “pathway docking” in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.
ISSN:0920-654X
1573-4951
DOI:10.1007/s10822-013-9675-1