MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular...

Phylogenetic tree construction from homologous sequences is a fundamental approach for studying evolutionary relationships. However, in cases where sequence similarity is too low to generate reliable alignments, comparison of protein structure provides an alternative means for inferring deep evolutionary relationships. MD-phylogeny is a method that integrates structural comparison with molecular dynamics (MD) simulations to generate robust phylogenies for protein datasets within the twilight zone of sequence similarity. This approach uses well-established structural superposition methods for building trees from structure, with a method for generating structural variants using MD simulations, from which confidence scores analogous to bootstrapping can be derived.This protocol provides a step-by-step guide to performing MD-phylogeny, covering dataset selection, structural comparisons, tree construction, and the generation of statistical support through MD simulations.