[Chimera-users] Autodock Vina tool in Chimera
gabsbi at rit.edu
Thu Jul 18 20:15:47 PDT 2019
Please keep it in Chimera...I do use it in class with Biomedical Engineering students learning molecular biology. I have them research drug target pathways at the KEGG website and then look for structures at PDB to try docking on.
they love the app
Greg at RIT
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, July 18, 2019 6:36 PM
To: Gregory Babbitt
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Autodock Vina tool in Chimera
We do not recommend it for most research purposes because it only allows a very small amount of sampling on a single ligand. I’ve tried to make this clear in the documentation:
Nothing against Autodock Vina per se, which is an excellent docking program. People should understand, however, that Autodock Vina is not developed by our group or included with Chimera, so we can’t answer all the questions that arise about it. Chimera’s Autodock Vina tool just connects to a web service running the program. As explained in the link above, the web service is provided by yet another group (neither us nor the Autodock Vina developers). Sampling is necessarily limited because the web service is a public (shared) resource.
You might ask, “so why is this tool even in Chimera?” We just discussed this due to the many recent questions and occasional misuses. There are some legitimate reasons:
(1) useful for students and docking novices to run a small example to learn about docking
(2) demo purposes, allows seeing a whole workflow in Chimera: Dock Prep -> docking -> ViewDock
(3) legitimate research purposes if a researcher is aware of the limitations: small ligand known or reasonably suspected to bind the protein, not too many rotatable bonds, known vicinity of binding (search box not too large), and/or additional pieces of evidence to corroborate the binding mode such as effects of mutations on binding, and/or small trial before embarking on more time-intensive docking with a dedicated docking program separate from Chimera
Of course, Dock Prep and ViewDock can also be used to prepare input for and view output of docking programs run separately.
I hope this clarifies the situation,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jul 18, 2019, at 3:13 PM, Gregory Babbitt <gabsbi at rit.edu> wrote:
> Can the autodock vina tool under structure/binding analysis be considered a reliable docking tool? It seems to go through the motions of docking just fine, but are the ligand positions returned by it really very stable?
> just curious
> Greg B
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