Background: The conventional superposition methods use an ordinary least squares (LS) fit forÂ structural comparison of two different conformations of the same protein. The main problem ofÂ the LS fit that it is sensitive to outliers, i.e. large displacements of the original structuresÂ superimposed.
Results: To overcome this problem, we present a new algorithm to overlap two proteinÂ conformations by their atomic coordinates using a robust statistics technique: least median of
squares (LMS). In order to effectively approximate the LMS optimization, the forward searchÂ technique is utilized. Our algorithm can automatically detect and superimpose the rigid core
regions of two conformations with small or large displacements. In contrast, most existingÂ superposition techniques strongly depend on the initial LS estimating for the entire atom sets of
proteins. They may fail on structural superposition of two conformations with large displacements.Â The presented LMS fit can be considered as an alternative and complementary tool for structural
Conclusion: The proposed algorithm is robust and does not require any prior knowledge of theÂ flexible regions. Furthermore, we show that the LMS fit can be extended to multiple level
superposition between two conformations with several rigid domains. Our fit tool has producedÂ successful superpositions when applied to proteins for which two conformations are known. The
binary executable program for Windows platform, tested examples, and database are availableÂ from https://engineering.purdue.edu/PRECISE/LMSfit.
Link to paper:Â Â http://www.biomedcentral.com/1471-2105/10/29
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