###### ## ## ## PhosMHCpred is a predictor for HLA-I - phosphorylated ligand interactions. ## ## CITATION: ## If you use PhosMHCpred in a publication, please cite: ## Solleder et al., MCP (2020). ## ## FOR-PROFIT USERS: ## If you plan to use PhosMHCpred or any data provided with the script in any for-profit ## application, you are required to obtain a separate license. To do so, please contact ## eauffarth@licr.org or lfoit@licr.org at the Ludwig Institute for Cancer Research Ltd. ## ## CONTACT: ## Marthe Solleder (marthe.solleder@unil.ch) and David Gfeller (david.gfeller@unil.ch). ## ## ###### ## PRELIMINARY Open the PhosMHCpred.py file and replace path (l. 35) by the path to the PhosMHCpred/ directory. ## COMMAND ./PhosMHCpred.py -p peptides -a alleles [-o output] To test PhosMHCpred: ./PhosMHCpred.py -p ./test/testPeptides.txt -a ./test/testAlleles.txt -o ./test/results.txt or: ./PhosMHCpred.py -p ./test/testPeptides.txt -a HLA-A0201,HLA-B4002 -o ./test/results.txt peptides [required]: File listing all the peptides or give a list of peptides in the command line separated by a single comma "," (e.g. ALLSRNHsL,FLIsKVEQI,GLYNsTDSL). alleles [required]: Define HLA-I allele for prediction (give as HLA-A0101). If predictions with more than one alleles are performed, give a file listing the alleles or list the alleles separated by a single comma (e.g. -a HLA-A0201,HLA-B4002). output [optional]: Give a name of the output file (if non given, results are saved as "results.txt" in current directory). ## OTHER INFORMATION - PhosMHCpred is trained on naturally presented phosphorylated and unmodified HLA-I ligands and gives a score for different peptides to identify the most likely HLA-I ligands for an allele (but does not predict affinity values). - The predictor can be run with more than one allele. In this case, the predictions are carried out for each allele separately and the predictor outputs independent results for the alleles. - The results are provided in [output]/results.txt