Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures

Rachel Kolodny, Patrice Koehl, Michael Levitt

Research output: Contribution to journalArticlepeer-review


We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called "Best-of-All" that combines the best results of all methods. Many commonly used methods miss 10-50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution.

Original languageEnglish
Pages (from-to)1173-1188
Number of pages16
JournalJournal of Molecular Biology
Issue number4
StatePublished - 4 Mar 2005
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health (GM063817) and National Science Foundation (CCR-00-86013). M.L. was also supported by the Fondation de l‘Ecole Normale Supérieure Chaires de Blaise Pascal. We are grateful to the authors of the structural alignment methods for making their programs available.


  • Comparison of structural alignment
  • Geometric measures
  • Protein structure alignment
  • Protein structure comparison
  • ROC curves

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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