[Chimera-users] AutoDock Vina Help

[Marco Sette]

Another useful server, especially for protein-protein and 
protein-nucleic acids, is Haddock.

https://haddock.science.uu.nl/

It is for biomolecular complex and is based on your experimental 
restraints (mutations, spectroscopic data, etc.).

Best

Marco

Il 23/06/2020 22:16, Elaine Meng ha scritto:
> Hi Ali,
> There are a huge number of docking programs: Autodock Vina, UCSF DOCK and many others. However, I don't know which can be used for RNA-protein docking vs. small molecule-protein or protein-protein docking, so you may need to investigate or literature-search that yourself.  I should also mention that the sampling that was allowed by the Autodock Vina web service was extremely unlikely to be sufficient for something as flexible and big as RNA, so I don't think that would have been the right tool for your question anyway.  You may have gotten a result but it wouldn't be a reliable indicator of reality.
>
> <http://vina.scripps.edu/>
> <http://dock.compbio.ucsf.edu/>
>
> You would need to obtain and use the docking program directly (not through a Chimera interface).  Then you may be able to look at the output using the ViewDock tool in Chimera. Not sure why  you mentioned PDB2PQR... I don't think that has anything to do with Autodock Vina.
>   
> If you want the ease of a web server (nothing to install yourself) a few are listed below.  However, again I do not know if they are intended or can be used for RNA-protein docking.
>
> SwissDock  <http://www.swissdock.ch/>
> Webina   <https://durrantlab.pitt.edu/webina/>
> DOCK Blaster <http://blaster.docking.org/>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Jun 23, 2020, at 8:46 AM, Ali <alikiyaei at gmail.com> wrote:
>>
>> Hi Everyone,
>>
>> As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling.
>>
>> Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist.
>>
>> Thank you,
>>
>> Ali from Cape Town
>
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-- 
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
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http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette