A General Substitution Matrix for Structural Phylogenetics.

ABSTRACT: Sequence-based maximum likelihood phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the evolutionary histories of proteins and the organisms that harbor them. However, modern implementations with sophisticated models of sequence evolution struggle to resolve deep evolutionary relationships, which can be obscured by excessive sequence divergence and substitution saturation. Structural phylogenetics has emerged as a promising alternative because protein structure evolves much more slowly than protein sequences. Recent developments in protein structure prediction using AI have made it possible to predict protein structures for entire protein families and then to translate these structures into a sequence representation-the 3Di structural alp

SUBMITTER: Garg SG 

PROVIDER: S-EPMC12198762 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature