What metric should we be using instead? RMSD? - ThreadSky | a Reddit-style client for Bluesky

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delalamo.xyz • 8 days ago

What metric should we be using instead? RMSD?

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bioinfo.se•8 days ago

We just changed d0 to be a constant of 5.0 (-d0 5.0 if you use USalign). But if you compare molecules of different sizes, you might need to run it twice (changing the order of query and target) or change a couple of lines in the code.

lindorfflarsen.bsky.social•8 days ago

What about eRMSD from Bottaro & Bussi https://doi.org/10.1093/nar/gku972 as implemented in barnaba https://github.com/srnas/barnaba

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