Hive mind: I seem to remember having seen a plot/analysis showing that pLDDT is correlated to conservation but my mind or Google-fu isn’t finding it - ThreadSky

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lindorfflarsen.bsky.social • 42 days ago

Hive mind:
I seem to remember having seen a plot/analysis showing that pLDDT is correlated to conservation but my mind or Google-fu isn’t finding it

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jgreener64.bsky.social•39 days ago

I also recall this plot but I can't remember where. The OpenFold paper (https://www.nature.com/articles/s41592-024-02272-z) has some performance comparisons against CATH holdout sets.

alexholehouse.bsky.social•35 days ago

We did this in our abf1 paper; main text shows correlation between disorder and conservation but then Fig. S3 shows histogram of correlation scores across yeast proteome where correlation here is pLDDT vs per residue conservation.

lindorfflarsen.bsky.social•35 days ago

Thanks! That's not the plot I was remembering, but it shows what I was thinking of, namely that low pLDDT in general to a substantial extent reflects low positional conservation (which of course is not that surprising)

carolinefwright.bsky.social•39 days ago

Did you find it? Would be interested to see if so... we've seen overall conservation relatively higher, and pLDDT lower, at N and C terminus, surprisingly.

lindorfflarsen.bsky.social•39 days ago

I am afraid not

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