TransHLA model TransHLA is a tool designed to discern whether a peptide will be recognized by HLA as an epitope. TransHLA is the first tool capable of directly identifying peptides as epitopes without the need for inputting HLA alleles. Due the different length of epitopes, we trained two models. The first is TransHLA I, which is used for the detection of the HLA I epitope, the other is TransHLA II, which is used for the detection of the HLA II epitope. Model description TransHLA is a hybrid transformer model that utilizes a transformer encoder module and a deep CNN module. It is trained using pretrained sequence embeddings from ESM2 and contact map structural features as inputs. It can serve as a preliminary screening for the currently popular tools that are specific for HLA epitope binding affinity. Intended uses Due to variations in peptide lengths, our TransHLA is divided into TransHLA I and TransHLA II, which are used to separately identify epitopes presented by HLA class I and class II molecules, respectively. Specifically, TransHLA I is designed for shorter peptides ranging from 8 to 14 amino acids in length, while TransHLA II targets longer peptides with lengths of 13 to 21…
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