Prediction of anti-inflammatory peptides by a sequence-based stacking ensemble model named AIPStack.
iScience 2022;
25:104967. [PMID:
36093066 PMCID:
PMC9449674 DOI:
10.1016/j.isci.2022.104967]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Accurate and efficient identification of anti-inflammatory peptides (AIPs) is crucial for the treatment of inflammation. Here, we proposed a two-layer stacking ensemble model, AIPStack, to effectively predict AIPs. At first, we constructed a new dataset for model building and validation. Then, peptide sequences were represented by hybrid features, which were fused by two amino acid composition descriptors. Next, the stacking ensemble model was constructed by random forest and extremely randomized tree as the base-classifiers and logistic regression as the meta-classifier to receive the outputs from the base-classifiers. AIPStack achieved an AUC of 0.819, accuracy of 0.755, and MCC of 0.510 on the independent set 3, which were higher than other AIP predictors. Furthermore, the essential sequence features were highlighted by the Shapley Additive exPlanation (SHAP) method. It is anticipated that AIPStack could be used for AIP prediction in a high-throughput manner and facilitate the hypothesis-driven experimental design.
AIPStack model was developed for the prediction of anti-inflammatory peptides
The hybrid features were used to describe the peptide sequences
The proposed model AIPStack outperformed existing ones
SHAP was used to highlight the essential features required for AIP prediction
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