Journal
FRONTIERS IN MICROBIOLOGY
Volume 9, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2018.00725
Keywords
modified cell-penetrating peptides; machine learning; Random Forest; SVM; in silico method; chemical descriptors; antimicrobial peptide
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Funding
- J. C. Bose National Fellowship (DST)
- Council of Scientific and Industrial Research (CSIR)
- Department of Science and Technology (DST-INSPIRE)
- Indian Council of Medical Research (ICMR)
- University Grant Commission (UGC)
- Department of Biotechnology (DBT)
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Designing drug delivery vehicles using cell-penetrating peptides is a hot area of research in the field of medicine. In the past, number of in silico methods have been developed for predicting cell-penetrating property of peptides containing natural residues. In this study, first time attempt has been made to predict cell-penetrating property of peptides containing natural and modified residues. The dataset used to develop prediction models, include structure and sequence of 732 chemically modified cell-penetrating peptides and an equal number of non-cell penetrating peptides. We analyzed the structure of both class of peptides and observed that positive charge groups, atoms, and residues are preferred in cell-penetrating peptides. In this study, models were developed to predict cell-penetrating peptides from its tertiary structure using a wide range of descriptors (2D, 3D descriptors, and fingerprints). Random Forest model developed by using PaDEL descriptors (combination of 2D, 3D, and fingerprints) achieved maximum accuracy of 95.10%, MCC of 0.90 and AUROC of 0.99 on the main dataset. The performance of model was also evaluated on validation/independent dataset which achieved AUROC of 0.98. In order to assist the scientific community, we have developed a web server CellPPDMod for predicting the cell-penetrating property of modified peptides (http://webs.iiitd.edu.in/raghava/cellppdmod/).
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