Statistical inference of protein structural alignments using information and compression

James H. Collier, Lloyd Allison, Arthur M. Lesk, Peter J. Stuckey, Maria Garcia De La Banda, Arun S. Konagurthu

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Motivation: Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. Results: We have implemented this approach in MMLigner, the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Availability and Implementation: Source code, binaries and an interactive web version are available at

Original languageEnglish (US)
Pages (from-to)1005-1013
Number of pages9
Issue number7
StatePublished - Apr 1 2017

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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