Intrinsic Disorder and Semi-disorder Prediction by SPINE-D

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Author(s)
Zhang, Tuo
Faraggi, Eshel
Li, Zhixiu
Zhou, Yaoqi
Griffith University Author(s)
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Zhou, Y
Kloczkowski, A
Faraggi, E
Yang, Y
Date
2017
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Abstract

Over the past decade, it has become evident that a large proportion of proteins contain intrinsically disordered regions, which play important roles in pivotal cellular functions. Many computational tools have been developed with the aim of identifying the level and location of disorder within a protein. In this chapter, we describe a neural network based technique called SPINE-D that employs a unique three-state design and can accurately capture disordered residues in both short and long disordered regions. SPINE-D was trained on a large database of 4229 non-redundant proteins, and yielded an AUC of 0.86 on a cross-validation test and 0.89 on an independent test. SPINE-D can also detect a semi-disordered state that is associated with induced folders and aggregation-prone regions in disordered proteins and weakly stable or locally unfolded regions in structured proteins. We implement an online web service and an offline stand-alone program for SPINE-D, they are freely available at http://​sparks-lab.​org/​SPINE-D/​. We then walk you through how to use the online and offline SPINE-D in making disorder predictions, and examine the disorder and semi-disorder prediction in a case study on the p53 protein.

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Prediction of Protein Secondary Structure
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Proteins and peptides
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Biochemistry and cell biology
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