The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement.

ABSTRACT: We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These are performed using the SKMT algorithm, a novel method of smoothing the Cα backbone to achieve a minimal complexity curve representation of the manner in which the protein's secondary structure elements fold to form its tertiary structure. Its subsequent complexity is characterised using measures based on the writhe and crossing number quantities heavily utilised in DNA topology studies, and which have shown promising results when applied to proteins recently. The SKMT smoothing is used to derive empirical bounds on a protein's entanglement relative to its number of secondary structure elements. We show that large scale he

SUBMITTER: Bale A 

PROVIDER: S-EPMC10703313 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature