AutoDock web site. AutoDock Vina Video Tutorial! This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL. Using AutoDock 4 and. Vina with. AutoDockTools: A Tutorial. Written by Ruth Huey, Garrett M. Morris and Stefano Forli. The Scripps Research. – AutoDock 4. Current version of AutoDock. Many parameters available to user. – AutoDock Vina. Rewritten by Oleg Trott, new approach to scoring.

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The hydrogens in the input file are used to decide which atoms can be hydrogen bond donors or acceptors though, so the correct protonation of the input structures is still important. The examples below assume that Bash is autosock shell. However, the source code, the scoring funcion and the actual algorithms used are brand new, so it’s more correct to think of AutoDock Vina as a new “generation” rather than “version” of AutoDock.

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Flexible Side Chains Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking. It also uses the same type of structure format PDBQT for maximum compatibility with auxiliary software.

AutoDock Vina – molecular docking and virtual screening program

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