Information about backbone atoms is lost when rebuilding full-atom protein models from alpha carbon trace alone

Summary

Backbone information is lost when coarse-grained models are rebuilt using only alpha carbons. (1) found that the N-C peptide bond tended to have 3x larger errors when rebuilt alpha carbons compared to when they are rebuilt from experimental density. CA-only ProteinMPNN showed a consistent 10% drop in sequence recovery compared to the default program, implying that it was unable to recover information provided by the explicit inclusion of other backbone atoms.

See also

• Alpha carbon-only representations are sufficient for ML force fields

1.

Heo L, Feig M. One particle per residue is sufficient to describe all-atom protein structures. openRxiv; 2023. Available from: https://doi.org/10.1101/2023.05.22.541652