DeepNeo: a webserver for predicting immunogenic neoantigens

Author:

Kim Jeong Yeon1,Bang Hyoeun2,Noh Seung-Jae2,Choi Jung Kyoon1ORCID

Affiliation:

1. Department of Bio and Brain Engineering, KAIST , Daejeon , Republic of Korea

2. PentaMedix Co., Ltd. , Seongnam-si , Gyeonggi-do , Republic of Korea

Abstract

Abstract Non-self epitopes, whether originated from foreign substances or somatic mutations, trigger immune responses when presented by major histocompatibility complex (MHC) molecules and recognized by T cells. Identification of immunogenically active neoepitopes has significant implications in cancer and virus medicine. However, current methods are mostly limited to predicting physical binding of mutant peptides and MHCs. We previously developed a deep-learning based model, DeepNeo, to identify immunogenic neoepitopes by capturing the structural properties of peptide-MHC pairs with T cell reactivity. Here, we upgraded our DeepNeo model with up-to-date training data. The upgraded model (DeepNeo-v2) was improved in evaluation metrics and showed prediction score distribution that better fits known neoantigen behavior. The immunogenic neoantigen prediction can be conducted at https://deepneo.net.

Funder

Basic Research Laboratory

Korea Drug Development Fund

Technology Development

Publisher

Oxford University Press (OUP)

Subject

Genetics

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