Computational protein–ligand docking and virtual drug screening with the AutoDock suite
| Autor: | Stefano Forli, Michael E. Pique, Michel F. Sanner, Ruth Huey, David S. Goodsell, Arthur J. Olson |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Computer science Drug Evaluation Preclinical Computational biology Ligands Bioinformatics 01 natural sciences Molecular Docking Simulation Article General Biochemistry Genetics and Molecular Biology Structure-Activity Relationship User-Computer Interface 03 medical and health sciences Scoring functions for docking Catalytic Domain Lead Finder Virtual screening 010405 organic chemistry Suite Proteins AutoDock 0104 chemical sciences 030104 developmental biology Protein–ligand docking Docking (molecular) Drug Design Software |
| Zdroj: | Nature Protocols. 11:905-919 |
| ISSN: | 1750-2799 1754-2189 |
| DOI: | 10.1038/nprot.2016.051 |
| Popis: | Computational docking can be used to predict bound conformations and free energies of binding for small molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction, and docking with explicit hydration. The entire protocol will require approximately 5 hours. |
| Databáze: | OpenAIRE |
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