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PCASSO: a fast and efficient C?-based method for accurately assigning protein secondary structure elements.


ABSTRACT: Proteins are often characterized in terms of their primary, secondary, tertiary, and quaternary structure. Algorithms such as define secondary structure of proteins (DSSP) can automatically assign protein secondary structure based on the backbone hydrogen-bonding pattern. However, the assignment of secondary structure elements (SSEs) becomes a challenge when only the C? coordinates are available. In this work, we present protein C-alpha secondary structure output (PCASSO), a fast and accurate program for assigning protein SSEs using only the C? positions. PCASSO achieves ?95% accuracy with respect to DSSP and takes ?0.1 s using a single processor to analyze a 1000 residue system with multiple chains. Our approach was compared with current state-of-the-art C?-based methods and was found to outperform all of them in both speed and accuracy. A practical application is also presented and discussed.

SUBMITTER: Law SM 

PROVIDER: S-EPMC4127665 | BioStudies | 2014-01-01

REPOSITORIES: biostudies

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