Relevant interacting amino acids between molecules
Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.
Dear Abisola, You can use the "Find Clashes/Contacts" tool or just a simple distance cutoff to find all the amino acid residues in one protein that are close to another molecule, which could be a small ligand, or another protein, DNA, etc. There is an example of using "FindHBond" and "Find Clashes/Contacts" to identify amino acids interacting with a ligand molecule in the "Structure Analysis and Comparison" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> It would be very similar to find the H-bonds and contacts between amino acids and some other kind of molecule (such as another protein), you would just need to select that other molecule instead of the ligand molecule. I think it will be clearer if you try that tutorial. Or, for simple cutoff you can first select one molecule and then use menu: Select... Zone to also select the nearby residues. Once they are selected, you can do other stuff with the Actions menu like labeling them, or getting a list of them as in the tutorial mentioned above. How to select: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> There is a more advanced example of using findclash (the command version of Find Clashes/Contacts) to color the atoms involved in a protein-protein interaction in the "Opened Interface" image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.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 Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote:
Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.
Dear Elaine, Thank you for the prompt response. I will go through the tutorials and I am sure it will be of great help. Thank you. Best Regards, Abisola Abisoye-Ogunniyan On Tue, Apr 15, 2014 at 5:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Abisola, You can use the "Find Clashes/Contacts" tool or just a simple distance cutoff to find all the amino acid residues in one protein that are close to another molecule, which could be a small ligand, or another protein, DNA, etc.
There is an example of using "FindHBond" and "Find Clashes/Contacts" to identify amino acids interacting with a ligand molecule in the "Structure Analysis and Comparison" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas...
It would be very similar to find the H-bonds and contacts between amino acids and some other kind of molecule (such as another protein), you would just need to select that other molecule instead of the ligand molecule. I think it will be clearer if you try that tutorial.
Or, for simple cutoff you can first select one molecule and then use menu: Select... Zone to also select the nearby residues. Once they are selected, you can do other stuff with the Actions menu like labeling them, or getting a list of them as in the tutorial mentioned above. How to select: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
There is a more advanced example of using findclash (the command version of Find Clashes/Contacts) to color the atoms involved in a protein-protein interaction in the "Opened Interface" image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.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 Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote:
Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.
participants (2)
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Elaine Meng -
Ogunniyan, Abisola