A SARS-CoV-2 Interaction Dataset and VHH Sequence Corpus for Antibody Language Models (2405.18749v3)

Abstract: Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases. To accelerate the discovery of antibody therapeutics, there is growing interest in constructing LLMs using antibody sequences. However, the applicability of pre-trained LLMs for antibody discovery has not been thoroughly evaluated due to the scarcity of labeled datasets. To overcome these limitations, we introduce AVIDa-SARS-CoV-2, a dataset featuring the antigen-variable domain of heavy chain of heavy chain antibody (VHH) interactions obtained from two alpacas immunized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins. AVIDa-SARS-CoV-2 includes binary labels indicating the binding or non-binding of diverse VHH sequences to 12 SARS-CoV-2 mutants, such as the Delta and Omicron variants. Furthermore, we release VHHCorpus-2M, a pre-training dataset for antibody LLMs, containing over two million VHH sequences. We report benchmark results for predicting SARS-CoV-2-VHH binding using VHHBERT pre-trained on VHHCorpus-2M and existing general protein and antibody-specific pre-trained LLMs. These results confirm that AVIDa-SARS-CoV-2 provides valuable benchmarks for evaluating the representation capabilities of antibody LLMs for binding prediction, thereby facilitating the development of AI-driven antibody discovery. The datasets are available at https://datasets.cognanous.com.