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normandavey / AlphaFold2-IDR-complex-prediction

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Linker usage #1

Open dypp1013 opened 3 years ago

dypp1013 commented 3 years ago

I want to predict the structure of a complex of 2 proteins, what linker should I use.

BalintMeszaros commented 3 years ago

In many cases I used a poly SG linker (i.e. SGSGSGSGSG) with 10-15 repeats (depending on protein size). However, AF2 allows the character U in the sequence so it's probably safest to use a bunch of Us linking the two sequences. So I now use a linker of 40 Us and that seems to gets the job done well.