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Structure Prediction of Partial-Length Protein Sequences
Department of Computer Science & Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195-7242, USA
* Author to whom correspondence should be addressed.
Received: 26 April 2013; in revised form: 1 July 2013 / Accepted: 2 July 2013 / Published: 17 July 2013
Abstract: 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
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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.
Laurenzi A, Hung L-H, Samudrala R. Structure Prediction of Partial-Length Protein Sequences. International Journal of Molecular Sciences. 2013; 14(7):14892-14907.
Laurenzi, Adrian; Hung, Ling-Hong; Samudrala, Ram. 2013. "Structure Prediction of Partial-Length Protein Sequences." Int. J. Mol. Sci. 14, no. 7: 14892-14907.