HLA-Clus: HLA class I clustering based on 3D structure.

ABSTRACT:

Background

In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria.

Results

The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained

SUBMITTER: Shen Y 

PROVIDER: S-EPMC10169335 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature