a community resource benchmarking predictions of peptide binding to mhc-i molecules社区资源的基准预测肽结合mhc i分子.pdfVIP

A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules 1* 1 2 2 2 1 1 Bjoern Peters , Huynh-Hoa Bui , Sune Frankild , Morten Nielsen , Claus Lundegaard , Emrah Kostem , Derek Basch , 3 3 1 1 1 2 3 Kasper Lamberth , Mikkel Harndahl , Ward Fleri , Stephen S. Wilson , John Sidney , Ole Lund , Soren Buus , 1 Alessandro Sette 1 La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America, 2 Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark, 3 Department of Experimental Immunology, Institute of Medical Microbiology and Immunology, University of Copenhagen, Copenhagen, Denmark Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here we make public a large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles. We use this data to establish a set of benchmark predictions with one neural network method and two matrix-based prediction methods extensively utilized in our groups. In general, the neural network outperforms the matrix-based predictions mainly due to its ability to generalize even on a small amount of data. We also retrieved predictions from tools publicly av