Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities

Abstract

For the characterization of various aspects of protein structures, four useful concepts are discussed: chameleon sequences, circular variance, mutual proximity, and a subsequence-based foldability score. These concepts were used in estimating foldability of globular, intrinsically disordered and fold-switching proteins, properties of protein-protein interfaces, quantifying sphericity, helping to improve protein-protein docking scores, and estimating the effect of mutations on stability. A conjecture about the Achilles' heel of proteins is presented as well.

Keywords: Amino acid propensity; Chameleon sequence; Circular variance; Foldability score; Mutual proximity.