How significant is a protein structure similarity with TM-score = 0.5?

MOTIVATION: Protein structure similarity is often measured by root mean squared deviation, global distance test score and template modeling score (TM-score). However, the scores themselves cannot provide information on how significant the structural similarity is. Also, it lacks a quantitative relation between the scores and conventional fold classifications. This article aims to answer two questions: (i) what is the statistical significance of TM-score? (ii) What is the probability of two proteins having the same fold given a specific TM-score? RESULTS: We first made an all-to-all gapless structural match on 6684 non-homologous single-domain proteins in the PDB and found that the TM-scores follow an extreme…

• NS
  National Science Foundation

  Awards: 0746198, DBI 0746198
• AP
  Alfred P. Sloan Foundation
• NI
  National Institute of General Medical Sciences

  Awards: GM083107, GM083107, GM084222, GM084222