Dynamical Fragments - Methods: Benchmarks

We benchmarked the condensed fragment libraries against their complete counterparts using an external data source, the Astral 40 structure compendium. We selected 1,000 fragments from a random set of PDBs and found their closest match by RMSD of N, Cα, Cβ, C, and O atoms. The condensed libraries contain nearly as many fragments as the complete sets, primarily reducing the size of the well-structured α-helical bins. Consequently, the condensed libraries perform nearly as well as the complete libraries in every case.