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BSLs can also monitor protein backbone motion with minimal complications from the internal flexibility of the side chain.
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During the simulations, the root mean square displacement (RMSD) on the protein backbone atoms and the area per lipid were monitored to ensure stable physical behavior.
As a result, under EX2 kinetic conditions, measurements of hydrogen exchange offer a direct monitor of the thermodynamic acidities of the amides along the protein backbone.
This method matches curvatures along the protein backbone.
In more general terms, protein backbone dynamics predictions could be related to functional information in proteins.
The predictions of protein backbone dynamics add another dimension to our knowledge about proteins.
In FRAGFOLD-IDP we introduce the idea of separating protein backbone dynamics from protein structure predictions.
Extended Data Fig. 7 Analysis of protein backbone dynamics during molecular dynamics equilibration and production.
Notably, DynaMine does not predict protein backbone dynamics directly, but approximates it using NMR order parameters.
In this work, we confirm that the de novo predictions of protein backbone dynamics are possible.
The compared vectors are those between adjacent α-carbons along the protein backbone.
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