chore: update from obsidian

Author: Spelkington

content/public/content/annotations/bertozzi-stickies.md

@@ -27,7 +27,7 @@ description: The rubber hits the road on ColabFold! I hope that's rubber I'm sme
 
 >%%
 >```annotation-json
->{"text":"Some context — Dr. Bertozzi was one of the the [2022 Nobel Laureates in Chemistry](https://www.nobelprize.org/prizes/chemistry/2022/bertozzi/facts/) for her contributions to developing [click](https://en.wikipedia.org/wiki/Click_chemistry) and [bioorthogonal](https://en.wikipedia.org/wiki/Bioorthogonal_chemistry) chemistries.\n\nMy understanding is that the basis for a lot of mucin research, especially in the synthesis space, is built on click chemistry — a general overview being that click chemistry is good for attaching complicated things to other complicated things. That explanation does the process zero justice, but it's the best I've got.","target":[{"source":"https://www.nature.com/articles/s41587-023-01840-6.pdf","selector":[{"type":"TextPositionSelector","start":622,"end":644},{"type":"TextQuoteSelector","exact":" Carolyn R. Bertozzi  ","prefix":"Weaver    4,9, Heinz Läubli2,3 &","suffix":"1,10  Targeted protein degrada"}]}],"created":"2026-02-28T19:55:01.027Z","updated":"2026-02-28T19:55:01.027Z","document":{"title":"Design of a mucin-selective protease for targeted degradation of cancer-associated mucins","link":[{"href":"urn:x-pdf:05688d5cb251214f88ff40cb330bdcef"},{"href":"https://www.nature.com/articles/s41587-023-01840-6.pdf"}],"documentFingerprint":"05688d5cb251214f88ff40cb330bdcef"},"uri":"https://www.nature.com/articles/s41587-023-01840-6.pdf"}
+>{"text":"Some context — Dr. Bertozzi was one of the the [2022 Nobel Laureates in Chemistry](https://www.nobelprize.org/prizes/chemistry/2022/bertozzi/facts/) for her contributions to developing [click](https://en.wikipedia.org/wiki/Click_chemistry) and [bioorthogonal](https://en.wikipedia.org/wiki/Bioorthogonal_chemistry) chemistries.\n\nMy understanding is that the basis for a lot of mucin research, especially in the synthesis space, is built on click chemistry — a general overview being that click chemistry is good for attaching complicated things to other complicated things. That explanation does the process zero justice, but it's the best I've got.\n\nThe catch, here, is that click chemistry attaches two complex structures together. If you're linking two big, rigid things together, you have some options in how flexible or stiff the connection point can be. The goal, then, is to use ColabFold to measure flexibility between two rigid structures.\n\nThe point of reading this paper is to look into ColabFold hyperparameters. Here, we have an established, published use of ColabFold for specifically this domain. If we can replicate the models, here, using the current hyperparameters (the defaults), then we can have some confidence that the current hyperparameters could apply well to other problems in this domain. If it doesn't match up, then we need to worry more about the hyperparameters.","target":[{"source":"https://www.nature.com/articles/s41587-023-01840-6.pdf","selector":[{"type":"TextPositionSelector","start":622,"end":644},{"type":"TextQuoteSelector","exact":" Carolyn R. Bertozzi  ","prefix":"Weaver    4,9, Heinz Läubli2,3 &","suffix":"1,10  Targeted protein degrada"}]}],"created":"2026-02-28T19:55:01.027Z","updated":"2026-02-28T19:55:01.027Z","document":{"title":"Design of a mucin-selective protease for targeted degradation of cancer-associated mucins","link":[{"href":"urn:x-pdf:05688d5cb251214f88ff40cb330bdcef"},{"href":"https://www.nature.com/articles/s41587-023-01840-6.pdf"}],"documentFingerprint":"05688d5cb251214f88ff40cb330bdcef"},"uri":"https://www.nature.com/articles/s41587-023-01840-6.pdf"}
 >```
 >%%
 >*%%PREFIX%%Weaver    4,9, Heinz Läubli2,3 &%%HIGHLIGHT%% ==Carolyn R. Bertozzi== %%POSTFIX%%1,10  Targeted protein degrada*
@@ -36,6 +36,10 @@ description: The rubber hits the road on ColabFold! I hope that's rubber I'm sme
 >Some context — Dr. Bertozzi was one of the the [2022 Nobel Laureates in Chemistry](https://www.nobelprize.org/prizes/chemistry/2022/bertozzi/facts/) for her contributions to developing [click](https://en.wikipedia.org/wiki/Click_chemistry) and [bioorthogonal](https://en.wikipedia.org/wiki/Bioorthogonal_chemistry) chemistries.
 >
 >My understanding is that the basis for a lot of mucin research, especially in the synthesis space, is built on click chemistry — a general overview being that click chemistry is good for attaching complicated things to other complicated things. That explanation does the process zero justice, but it's the best I've got.
+>
+>The catch, here, is that click chemistry attaches two complex structures together. If you're linking two big, rigid things together, you have some options in how flexible or stiff the connection point can be. The goal, then, is to use ColabFold to measure flexibility between two rigid structures.
+>
+>The point of reading this paper is to look into ColabFold hyperparameters. Here, we have an established, published use of ColabFold for specifically this domain. If we can replicate the models, here, using the current hyperparameters (the defaults), then we can have some confidence that the current hyperparameters could apply well to other problems in this domain. If it doesn't match up, then we need to worry more about the hyperparameters.
 >%%TAGS%%
 >
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