Minimum Message Length Inference of Secondary Structure from Protein Coordinate Data

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 ISMB 11

Arun S. Konagurthu, Arthur M. Lesk, Lloyd Allison

J. Bioinformatics, 28(12), pp.i97-i105, June 2012   (ISMB, July 2012).

Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data.
Results: We report a new method to infer secondary structure based on the Bayesian method of Minimum Message Length (MML) inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximise the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it to popular programs such as DSSP and STRIDE amongst others. Our evaluation suggests that SST gives reliable assignments even on low resolution structures.
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