opencadd.structure.superposition.engines.theseus

Description

Theseus superposes a set of macromolecular structures simultaneously using the method of maximum like-lihood (ML), rather than the conventional least-squares criterion. Theseus assumes that the structures are distributed according to a matrix Gaussian distribution and that the eigenvalues of the atomic covariancematrix are hierarchically distributed according to an inverse gamma distribution. This ML superpositioning model produces much more accurate results by essentially downweighting variable regions of the structuresand by correcting for correlations among atoms.

References

  • https://theobald.brandeis.edu/theseus/

  • Optimal simultaneous superpositioning of multiple structures with missing data. Theobald, Douglas L. & Steindel, Philip A. (2012) Bioinformatics 28 (15): 1972-1979

  • Accurate structural correlations from maximum likelihood superpositions. Theobald, Douglas L. & Wuttke, Deborah S. (2008) PLOS Computational Biology 4(2):e43

Classes

TheseusAligner([sequence_alignment, ...])

Superpose structures with different sequences but similar structures