Jul 2026· Journal of Applied Crystallography· 0 citations
TL;DR
This method enables rapid and accurate identification of structural repeats by calculating the distance between Cα atoms in the peptide backbone by calculating the distance between Cα atoms in the peptide backbone.
Abstract
Repeats in protein structures act as essential structural building blocks, commonly forming multiple complex structures and functional units. Identifying sequence repeats in the primary structure alone is not sufficient to find the function of the proteins. Therefore, a new method, repeats in the three-dimensional structure of proteins (
Rep3D
), has been developed using a dynamic programming approach. This method enables rapid and accurate identification of structural repeats by calculating the distance between Cα atoms in the peptide backbone. A standalone computing version of the tool has been developed and implemented in Python. The
Rep3D
source code, along with documentation, examples of use and instructions, is available in the
Rep3D
repository (https://github.com/srimaha0801/Rep3d-Stand_Alone_v1/).
An in-depth analysis of tandem and non-tandem repeats observed in a non-redundant set of 378 protein-DNA complexes archived in the Protein Data Bank reveals that the former is shorter, exhibit reduced variability and facilitate structural conservation.
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