Supplemental Data for "High-throughput screening for class I peptide–MHC binding via yeast surface display" (Holec et al., 2025)

This dataset contains the full supplementary materials for the study “High-throughput screening for class I peptide–MHC binding via yeast surface display” (Holec et al., 2025). It includes raw and processed data, reference sequences, oligo pools, NetMHC predictions, peptide enrichment data, and figures associated with benchmarking and pathogen screening. Raw sequencing files are publicly accessible at the NIH Sequence Read Archive under accession SUB15276783. Directory overview: references/ selected_alleles.xlsx — listing of wild-type class I MHC sequences all_alleles.csv — listing of wild-type class I MHC sequences ngs_sample_sheet_overview.xlsx — overview of demultiplexing settings for each pooled library included in raw sequence files for the study (raw FASTQ files accessible at the NIH Sequence Read Archive, SUB15276783) references/oligo_pools/ nnk-benchmark_oligo-pool-overview.csv — descriptive data for peptides used in the benchmarking library nnk-benchmark_oligo-pool-order.fasta — submitted oligo synthesis file for peptides included in benchmarking libraries pathogen-screen_oligo-pool-order.fasta — submitted oligo synthesis file for peptides included in pathogen libraries references/reference_genomes/ (4 folders) — references for all genomes used in the pathogen screening study datasets/netmhc_peptide_predictions/ (35 files) — NetMHC binding affinity and eluted rank for peptides included in the pathogen screen datasets/nnk_benchmark_library_datasets/ nnk_read_counts.csv — read counts for peptides screened in NNK libraries for each tested MHC allele Benchmark_read_counts.xlsx — frequencies for defined peptides included in the benchmark study, paired retrieved database data (IEDB / Kd) datasets/nnk_benchmark_library_datasets/enrichment_figures/ (66 files) — sequence logos and heatmaps for each allele screened in the NNK + benchmark screens datasets/pathogen_library_cutoffs/ (83 files) — binary classifier figures for peptides in each allele included in the pathogen screening study datasets/pathogen_library_datasets/ all_pathogen_positives.xlsx — list of positive peptide binders found for each allele in the pathogen screen (as defined by binary classifier) pathogen_enrichments.xlsx — enrichments of each peptide by allele in the pathogen screening study pathogen_library_ranks.xlsx — ordered ranks of each peptide by allele in the pathogen screening study pathogen_read_counts.xlsx — read counts of each peptide by allele in the pathogen screening study datasets/pathogen_library_datasets_by_gene/ (32 files) — probability and binary classification of peptides included in the pathogen library screen, divided by genome source datasets/pathogen_library_images/ (438 files) — heatmaps of each gene derived from Mtb T7SS substrates, Dengue, Zika, and SARS-CoV-2 genomes included in the screening study