[Chimera-users] Ligand Receptor docking

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 19 12:39:15 PST 2018

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:
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.
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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