ProPred1

[…] bayes empirical bayes (beb) analysis, the sites with the posterior probability > 95% were identified as the positively selected sites [–]., the propred-i server (http://www.imtech.res.in/raghava/propred1/) and propred server (http://www.imtech.res.in/raghava/propred/) were used to predict the major histocompatibility complex (mhc) class-i binding peptides [] and mhc class-ii binding peptides […]

[…] the optimized gene was subcloned into pet28a expression vector (novagen, u.s.). according to active site (pdb code 2sak and 1bui) and epitope predication (propred-i, http://www.imtech.res.in/raghava/propred1/) [, ], five candidate pegylation sites were selected and mutant to cysteine, including c79g, c82l, c84k, c97a, and c104r, respectively. the mutant sak gene was amplified from the optimized […]

[…] t cell epitope prediction. , ctlpred (http://www.imtech.res.in/raghava/ctlpred/), which is an ann and svm based ctl epitope prediction tool. , propred-i (http://www.imtech.res.in/raghava/propred1/-), which predicts mhc-i binding regulation in an antigen sequence using quantitative matrices for 47 mhc-i alleles. , propred (www.imtech.res.in/raghava/propred/), which predicts mhc-ii […]

[…] unique e6/e7 have been described in previous studies [,–]. numbers above the branches indicated the bootstrap values that are greater than 75%., propred-i server (http://www.imtech.res.in/raghava/propred1/) [] was used to predict the human leukocyte antigen (hla) class i binding promiscuous epitope(s) at the default settings (allele selection: all, threshold: 4%, tabular results: 4, […]

[…] predicted using ctlpred and nhlapred, which were present in more than 800 unique cell lines ( and tables). also, there were more than 15 neopeptides found to be hla class i binders (using propred1) from recql4 and prkdc, which were present in more than 600 cell lines (). similarly, in case of hla class ii binders (propred), pde4dip has 7 or more neoepitopes (hla class ii), […]