Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features

BMC Bioinformatics

Research

Yaohang Li¹  Ashraf Yaseen¹ 

[1] Department of Computer Science, Old Dominion University, 23529, Norfolk, VA, USA;

关键词: Secondary Structure;    Prediction Accuracy;    Protein Data Bank;    Secondary Structure Prediction;    Neural Network Training;   

DOI  :  10.1186/1471-2105-15-S8-S3

来源: Springer

【 摘 要 】

BackgroundSecondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.MethodsIn this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead.ResultsAfter applying the template-based 8-state secondary structure prediction method, the 7-fold cross-validated Q8 accuracy is 78.85%. Even templates from structures with only 20%~30% sequence similarity can help improve the 8-state prediction accuracy. More importantly, when good templates are available, the prediction accuracy of less frequent secondary structures, such as 3-10 helices, turns, and bends, are highly improved, which are useful for practical applications.ConclusionsOur computational results show that the templates containing structural information are effective features to enhance 8-state secondary structure predictions. Our prediction algorithm is implemented on a web server named "C8-SCORPION" available at: http://hpcr.cs.odu.edu/c8scorpion.

【 授权许可】

CC BY   
© Yaseen and Li; licensee BioMed Central Ltd. 2014