New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
Hi Chimera users, I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein. https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Glob... @Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html <https://www.cgl.ucsf.edu/chimera/tutorials.html>? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time. With best regards, Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
Hi Thomas, Thanks for creating the tutorial! Yes, we can add it to the Chimera tutorials page (I will send you a link privately to preview). If you are planning to make several such tutorials available, it would be best if you could create an index page that lists all of your tutorials with short descriptions. Then our Chimera tutorials page can link to your index, and users will be able to see the list with all of your latest additions and updates without our having to update our own page this time. There is some overhead since I try to put descriptions and images with each. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 10, 2019, at 9:31 AM, Thomas Evangelidis <tevang3@gmail.com> wrote:
Hi Chimera users,
I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein.
https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Glob...
@Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html ? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time.
With best regards, Thomas
-- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague, Czech Republic & CEITEC - Central European Institute of Technology Brno, Czech Republic
email: tevang3@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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participants (2)
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Elaine Meng -
Thomas Evangelidis