Protsubs: a series of substitution matrices reflecting relationships between protein evolution and structure

Abstract

Protein sequence matching is a fundamental step in many bioinformatics approaches. Amino acid substitution matrices developed decades ago, such as BLOSUM series matrices, are still commonly used in most present-day applications. With the accumulation of many protein structures and huge sequence data, together with advances in understanding protein mechanisms, there is a huge opportunity for improving amino acid substitution matrices. Previously, our group developed the ProtSub (Protein Substitutions) matrix (Jia, Jernigan, Proteins: Structure, Function, and Bioinformatics, 89(6), 2021) that utilizes the existing structural information and knowledge of sequence coevolution correlations.