CATS: A Tool for Clustering the Ensemble of Intrinsically Disordered Peptides on a Flat Energy Landscape.

ABSTRACT: We introduce the combinatorial averaged transient structure (CATS) clustering method as a means to cluster protein structure ensembles based on the distributions of protein backbone descriptor coordinates. In our study, we use phi and psi dihedral angle coordinates of the protein backbone as descriptors due to their translational and rotational invariance. The CATS method was developed to produce unique structure ensembles that are typically difficult to obtain from flat energy landscapes using a one-dimensional separation value (e.g., RMSD cutoff). Through the use of higher-dimensional descriptor coordinates, we remedy structure resolution shortcomings of standard clustering algorithms due to large RMSD fluctuations between structures. We compare the performance of CATS to an RMSD-based c

SUBMITTER: Ezerski JC 

PROVIDER: S-EPMC7155914 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature