PT  - JOURNAL ARTICLE
AU  - Gandharva Nagpal
AU  - Kumardeep Chaudhary
AU  - Piyush Agrawal
AU  - Gajendra P.S. Raghava
TI  - Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants
AID  - 10.1101/232025
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 232025
4099  - http://biorxiv.org/content/early/2017/12/11/232025.short
4100  - http://biorxiv.org/content/early/2017/12/11/232025.full
AB  - Background Evidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants. All the mechanisms of vaccine adjuvants ensuing immunostimulatory effects directly or indirectly stimulate Antigen Presenting Cells (APCs). While numerous methods have been developed in the past for predicting B-cell and T-cell epitopes; no method is available for predicting the peptides that can modulate the APCs.Methods We named the peptides that can activate APCs as A-cell epitopes and developed methods for their prediction in this study. A dataset of experimentally validated A-cell epitopes was collected and compiled from various resources. To predict A-cell epitopes, we developed Support Vector Machine-based machine learning models using different sequence-based features.Results A hybrid model developed on a combination of sequence-based features (dipeptide composition and motif occurrence), achieved the highest accuracy of 96.91% with Matthews Correlation Coefficient (MCC) value of 0.94 on the training dataset. We also evaluated the hybrid models on an independent dataset and achieved a comparable accuracy of 94.93% with MCC 0.90.Conclusion The models developed in this study were implemented in a web-based platform VaxinPAD to predict and design immunomodulatory peptides or A-cell epitopes. This web server available at http://webs.iiitd.edu.in/raghava/vaxinpad/ and http://crdd.osdd.net/raghava/vaxinpad/ will facilitate researchers in designing peptide-based vaccine adjuvants.APCAntigen Presenting CellPRRPattern Recognition ReceptorHDPHost Defense PeptideIDRInnate Defense RegulatorTLRToll-like receptorCAMPCathelicidin Antimicrobial PeptideMHCMajor Histocompatibility ComplexSVMSupport Vector MachineMERCIMotif—EmeRging and with Classes—IdentificationTSLTwo-Sample LogoCPPCell Penetrating Peptides