RDb(2)C2: an improved method to identify the residue-residue pairing in β strands

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 RDb(2)C 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, RDb(2)C2, 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 RDb(2)C2 at http://structpred.life.tsinghua.edu.cn/rdb2c2.html.