Drug-Protein Interaction
Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*
Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*
Hi Kanika, Take a look at the ViewDock tutorial. It looks at H-bonds between ligand and receptor using the FindHBond tool. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/vdtut.html> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findhbond/findhbond.html> Another tool that might be useful for this purpose is Find Clashes/Contacts (in menu under Tools... Surface/Binding Analysis): <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/findclash.html> I also recommend doing the Structure Analysis and Comparison tutorial, which uses distance measurements, FindHBond, Find Clashes/Contacts etc. to examine a binding pocket: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/squalene.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 18, 2013, at 3:34 AM, kanika sharma wrote:
Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- Regards, Kanika Sharma
Please see previous answer to same question: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-February/008461.html> On Feb 18, 2013, at 3:24 AM, kanika sharma wrote:
Hi All,
I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position?
-- Regards,
Kanika Sharma
On 02/20/2013 02:49 AM, Elaine Meng wrote:
Please see previous answer to same question: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-February/008461.html>
There is the ligplot software also. Might be nice to have plugged into Chimera.
On Feb 18, 2013, at 3:24 AM, kanika sharma wrote:
Hi All,
I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position?
-- Regards,
Kanika Sharma
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Thank you all for the answers. That is really helpful On Wed, Feb 20, 2013 at 1:29 AM, Francois Berenger <berenger@riken.jp>wrote:
On 02/20/2013 02:49 AM, Elaine Meng wrote:
Please see previous answer to same question: <http://plato.cgl.ucsf.edu/**pipermail/chimera-users/2013-** February/008461.html<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-February/008461.html>
There is the ligplot software also. Might be nice to have plugged into Chimera.
On Feb 18, 2013, at 3:24 AM, kanika sharma wrote:
Hi All,
I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position?
-- Regards,
Kanika Sharma
______________________________**_________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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-- *Regards,* * * *Kanika Sharma*
participants (3)
-
Elaine Meng -
Francois Berenger -
kanika sharma