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Extracting annotations from structures #8
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@all-contributors please add @BarbaraTerlouw for ideas As I expect this effort to include contributions from several people, please feel free to acknowledge them using the all-contributors bot at described in the contribution guidelines |
I've put up a pull request to add @BarbaraTerlouw! 🎉 |
Added a notebook https://github.com/BarbaraTerlouw/covid19/blob/master/Ensemble.ipynb to analyze the variability in RMSD between the different versions of the SARS-Cov2 3CL-PRO protein (with different ligands bound), and a SARS-Cov 3CL-PRO protein. |
Update on progress:
Example annotations on 3CL-pro (main protease):
To be able to see each of these annotations:
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Nice work. Thanks. On our end we are discussing display issues since by default per-residue annotations get a ball-and-stick display which doesn't really work well for your type of data. As a temp. workaround for the NGL 3D viewer: if you select "Cartoon" view after selecting the annotations you can get rid of the sticks. |
@all-contributors please add @mlgill for solvent accessibility and interface annotations |
I've put up a pull request to add @mlgill! 🎉 |
@akdel Do we know the direction of movement from your calculations? I've seen it done by varying the width of the backbone for NMR spin relaxation measurements, etc. |
The direction is stored per residue for a given time in normal mode data format. Some more context here. Did I understand your question correctly? |
Yes, that's my question. Thanks -- I was trying to understand how specific the directionality was or if it was more indicative of the magnitude of motions. Sounds like the former. |
Have pushed a draft of the code to extract surface accessibility values and write a CSV for a given PDB. What else is needed? Feedback welcome. Thanks. |
Very cool! We can pull your code and add a small function to generate a SWISS-MODEL annotation URL that visualizes the accessibility on the structure if you'd like. I guess we can move on to the integrating other issues? Interface residues or glycosylation sites are still open as far as I can see. Do you have any other ideas? |
@Ninjani I'm happy to work on adding the SWISS-MODEL annotation URL to my current PR, if you'd like. This code looks like a reference for how to do that, unless you have another example in mind? After that I'll look into the glycosylation sites work. |
Yes, I think you can use this script from the utils folder combined with the Okay, cool! |
Currently working on incorporating the solvent accessibility measurements into @Ninjani 's framework. Had several work interruptions today, but will finish debugging and testing tomorrow. |
@Ninjani Could you verify that the branch I should be pulling code from in your fork is "master" and not "utils"? Thank you! |
@all-contributors please add @akdel for code |
I've put up a pull request to add @akdel! 🎉 |
@all-contributors please add @mlgill for code |
I've put up a pull request to add @mlgill! 🎉 |
By: Barbara Terlouw, Mehmet Akdel, Janani Durairaj
These are the annotation types/sources that we are planning to work on. We'll be writing scripts such that the annotations can be generated for any PDB file so that it works for new ones as well. These annotations are mostly per structure, per residue, except for the first two. Suggestions welcome!
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