DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies
Issued Date
2022-01-01
Resource Type
ISSN
15455963
eISSN
15579964
Scopus ID
2-s2.0-85112628148
Pubmed ID
34347603
Journal Title
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume
19
Issue
5
Start Page
2749
End Page
2759
Rights Holder(s)
SCOPUS
Bibliographic Citation
IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol.19 No.5 (2022) , 2749-2759
Suggested Citation
Arif M., Kabir M., Ahmed S., Khan A., Ge F., Khelifi A., Yu D.J. DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol.19 No.5 (2022) , 2749-2759. 2759. doi:10.1109/TCBB.2021.3102133 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/83953
Title
DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies
Other Contributor(s)
Abstract
Cell-penetrating peptides (CPPs) are special peptides capable of carrying a variety of bioactive molecules, such as genetic materials, short interfering RNAs and nanoparticles, into cells. Recently, research on CPP has gained substantial interest from researchers, and the biological mechanisms of CPPS have been assessed in the context of safe drug delivery agents and therapeutic applications. Correct identification and synthesis of CPPs using traditional biochemical methods is an extremely slow, expensive and laborious task particularly due to the large volume of unannotated peptide sequences accumulating in the World Bank repository. Hence, a powerful bioinformatics predictor that rapidly identifies CPPs with a high recognition rate is urgently needed. To date, numerous computational methods have been developed for CPP prediction. However, the available machine-learning (ML) tools are unable to distinguish both the CPPs and their uptake efficiencies. This study aimed to develop a two-layer deep learning framework named DeepCPPred to identify both CPPs in the first phase and peptide uptake efficiency in the second phase. The DeepCPPred predictor first uses four types of descriptors that cover evolutionary, energy estimation, reduced sequence and amino-acid contact information. Then, the extracted features are optimized through the elastic net algorithm and fed into a cascade deep forest algorithm to build the final CPP model. The proposed method achieved 99.45 percent overall accuracy with the CPP924 benchmark dataset in the first layer and 95.43 percent accuracy in the second layer with the CPPSite3 dataset using a 5-fold cross-validation test. Thus, our proposed bioinformatics tool surpassed all the existing state-of-the-art sequence-based CPP approaches.