PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score.

ABSTRACT:

Motivation

Evolutionary inference depends crucially on the quality of multiple sequence alignments (MSA), which is problematic for distantly related proteins. Since protein structure is more conserved than sequence, it seems natural to use structure alignments for distant homologs. However, structure alignments may not be suitable for inferring evolutionary relationships.

Results

Here we examined four protein similarity measures that depend on sequence and structure (fraction of aligned residues, sequence identity, fraction of superimposed residues, and contact overlap), finding that they are intimately correlated but none of them provides a complete and unbiased picture of conservation in proteins. Therefore, we propose the new hybrid protein sequence and structure similari

SUBMITTER: Bastolla U 

PROVIDER: S-EPMC10628387 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature