[Chimera-users] Ligand Receptor docking

[Elaine Meng]

Hi Pratik,
We have lists of Chimera citations (partial list on our website here)
<http://www.rbvi.ucsf.edu/chimera/citations.html>

… but as I said before, we are not the developers of Autodock Vina.  The docking is not done inside of Chimera.  Chimera just sends the structures to the outside web service and waits for the results to come back.

Regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 19, 2018, at 6:06 PM, Shriwas, Pratik <ps774614 at ohio.edu> wrote:
> 
> Hi,
> 
> Thank you for your advice. I am grateful that you have let me know about the literature. I am sorry if it was offending for me to ask for papers.
> 
> I meant that sometimes when companies offer their products, they put a citations list. So, I asked. I am sorry.
> 
> Regards,
> Pratik
> 
> Get Outlook for Android
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Monday, November 19, 2018 9:01:10 PM
> To: Shriwas, Pratik
> Cc: chimera-users
> Subject: Re: [Chimera-users] Ligand Receptor docking
>  
> Sorry, you will have to do your own literature searching!  This address is for help in using Chimera, not general research advice.  My statement was based on seeing Autodock Vina mentioned in many research papers over the years, but I don’t have a specific list.  You could just search for keywords like “vina” or “autodock vina”.  However,  people who use Autodock Vina are not necessarily using Chimera or the web service; many people download that software and use it directly.  It is developed by a group at Scripps:
> <http://vina.scripps.edu/index.html>
> 
> Regards,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Nov 19, 2018, at 12:51 PM, Shriwas, Pratik <ps774614 at ohio.edu> wrote:
> > 
> > Thank you!
> > 
> > Can you send me some publications list which used Chimera (autodock vina). Is there a link where I can find this?
> > 
> > Regards,
> > 
> > Pratik Shriwas
> > Phd Candidate,
> > Molecular and Cellular Biology program,
> > Edison Biotechnology Institute,
> > Ohio University.
> > 
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Monday, November 19, 2018 3:39:15 PM
> > To: Shriwas, Pratik
> > Cc: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Ligand Receptor docking
> >  
> > Hi Pratik Shriwas,
> > You have to use your own scientific judgment for questions like this.  If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help:
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> > Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people.
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > > On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614 at ohio.edu> wrote:
> > > 
> > > Hi,
> > > I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
> > > 
> > > I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
> > > 
> > > I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email.
> > > Thank you.
> > > Regards,
> > > 
> > > Pratik Shriwas
> > > Phd Candidate,
> > > Molecular and Cellular Biology program,
> > > Edison Biotechnology Institute,
> > > Ohio University.
> > 
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