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Int. J. Mol. Sci. 2013, 14(7), 14892-14907; doi:10.3390/ijms140714892

Structure Prediction of Partial-Length Protein Sequences

1 Department of Computer Science & Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA 2 Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195-7242, USA
* Author to whom correspondence should be addressed.
Received: 26 April 2013 / Revised: 1 July 2013 / Accepted: 2 July 2013 / Published: 17 July 2013
(This article belongs to the Special Issue Protein Folding 2015)
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Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs) that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence (“foldability”). This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.
Keywords: protein structure prediction; EST; expressed sequence tag; protein folding; protein design protein structure prediction; EST; expressed sequence tag; protein folding; protein design
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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Laurenzi, A.; Hung, L.-H.; Samudrala, R. Structure Prediction of Partial-Length Protein Sequences. Int. J. Mol. Sci. 2013, 14, 14892-14907.

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