Dear Dr. Samson, The web service used by Chimera is more restricted than if you run Autodock Vina separately. If you run it separately (e.g. download Autodock Vina and run it on your own computer) you can increase the sampling much more than the web service allows, which would increase the chances of meaningful results. I don’t see many details about input docking parameters in that paper you mentioned, but since they said they used high-performance computing, they probably did fairly long calculations. It is hard to reproduce results if they don’t tell you all the input settings for the calculations. I hope this clarifies the situation, Elaine
On Oct 23, 2017, at 6:08 PM, Dr. Samson Soon <samson@iukl.edu.my> wrote:
Dear Dr. Elaine
Thank you so much for your generous insights. As you probably know, I'm very new to all these. I'm trying to simulate the results of a published work using autodock vina & other docking systems on RNA aptamers (https://www.nature.com/articles/srep21285). The binding affinities of the RNA ligands were predicted and scored using these approaches. I'm surprised as autodock vina was featured prominently in their report for all virtual docking experiments analyzed. I will follow up on your suggestions and compare the outcome. Thanks again for your kind help.
Best regards
DR. SAMSON SOON I Director Research Management Center (RMC) Infrastructure University Kuala Lumpur (IUKL) Office: +603.8738.3388 ext 374 Mobile: +6016.221.8010 www.IUKL.edu.my l myIUKL l @myIUKL
On Tue, Oct 24, 2017 at 2:07 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Samson, I do not think you can use this tool for what you want to do. Your “ligand” is an RNA, large, with many rotatable bonds. The Autodock Vina web service accessed by Chimera only allows a very small amount of sampling, even for a small organic molecule (like a drug) and I do not think you would be able to get any scientifically meaningful results on this protein-RNA system.
I don’t even know if Vina is meant for protein-RNA docking… if so, you would need to download it yourself (to allow adjusting more parameters and increasing the sampling higher than what the web service allows). Here is the Autodock Vina website, for download and for asking questions about the program: <http://vina.scripps.edu/>
If you only want an easy web-service approach instead of installing the docking program yourself, it might be possible with the Hex server or HADDOCK, but I haven’t tried these myself and don’t know if they work with protein-RNA either:
Hex <http://hexserver.loria.fr/>
HADDOCK (requires registration) <http://milou.science.uu.nl/services/HADDOCK2.2/>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco