@article{open2189,
          volume = {9},
           month = {April},
          author = {Vinod Kumar and Piyush Agrawal and Rajesh Kumar and Sherry Bhalla and Salman Sadullah Usmani and Grish C Varshney and Gajendra P S Raghava},
           title = {Prediction of Cell-Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues.},
       publisher = {Frontiers Media S.A},
         journal = {Frontiers in microbiology},
           pages = {725},
            year = {2018},
        keywords = {Random Forest; SVM; antimicrobial peptide; chemical descriptors; in silico method; machine learning; modified cell-penetrating peptides},
             url = {http://crdd.osdd.net/open/2189/},
        abstract = {Designing drug delivery vehicles using cell-penetrating peptides is a hot area of research in the field of medicine. In the past, number of  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/).}
}