search

Rappsilber-Laboratory / AlphaLink2

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer
Creative Commons Attribution 4.0 International
42 stars 11 forks source link

Incorporation of monolinks #21

Open enriquead1 opened 4 months ago

enriquead1 commented 4 months ago

I have just read the paper cited at the end, and it convinced me about the potential of monolinks as a source of experimental information regarding surface accessibility. As suggested there, this may be especially powerful on small proteins where cross-links are unlikely. Could this be implemented on Alphalink? What about monolink recovery on XiSearch?

Manalastas-Cantos, K., Adoni, K. R., Pfeifer, M., Märtens, B., Grünewald, K., Thalassinos, K., & Topf, M. (2024). Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry. Molecular & Cellular Proteomics. https://doi.org/10.1016/j.mcpro.2024.100724

lhatsk commented 4 months ago

Thanks for pointing this out! Are there large-ish datasets available? It could be implemented in AlphaLink, but it's not in our plans at the moment. I could see it already working to some degree if you encode monolinks as self-links in the SDA network.

enriquead1 commented 4 months ago

You are welcome! Thank you for this work. The same datasets with crosslinks contain also monolinks (crosslinks where only one of the reactive groups reacted). I have been checking XiFDR results and it does not seem too hard to extract them from _Linear_PSM_xiFDR files, as there is a "PepSeq1" column that includes the crosslinker when it is present.