RDb2C2: an improved method to identify the residue-residue pairing in β strands

Autor: Yaoguang Xing, Di Shao, Haipeng Gong, Wenzhi Mao
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-12 (2020)
ISSN: 1471-2105
DOI: 10.1186/s12859-020-3476-z
Popis: Background Despite the great advance of protein structure prediction, accurate prediction of the structures of mainly β proteins is still highly challenging, but could be assisted by the knowledge of residue-residue pairing in β strands. Previously, we proposed a ridge-detection-based algorithm RDb2C that adopted a multi-stage random forest framework to predict the β-β pairing given the amino acid sequence of a protein. Results In this work, we developed a second version of this algorithm, RDb2C2, by employing the residual neural network to further enhance the prediction accuracy. In the benchmark test, this new algorithm improves the F1-score by > 10 percentage points, reaching impressively high values of ~ 72% and ~ 73% in the BetaSheet916 and BetaSheet1452 sets, respectively. Conclusion Our new method promotes the prediction accuracy of β-β pairing to a new level and the prediction results could better assist the structure modeling of mainly β proteins. We prepared an online server of RDb2C2 at http://structpred.life.tsinghua.edu.cn/rdb2c2.html.
Databáze: OpenAIRE
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