Published February 6, 2026
| Version v1
Model
Open
Mapping of Conformational Epitopes on SARS-CoV-2 Antigens Targeted by Monoclonal Antibodies
Authors/Creators
- 1. Chulalongkorn University Faculty of Pharmaceutical Sciences
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2.
Chulalongkorn University
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3.
King Chulalongkorn Memorial Hospital
Description
The spike glycoprotein of SARS-CoV-2, particularly its receptor-binding domain (RBD), is a primary target for therapeutic monoclonal antibodies (mAbs). In this study, AlphaFold was used to generate structural models of SARS-CoV-2 spike protein variants to support the interpretation of diethylpyrocarbonate covalent labeling mass spectrometry (DEPC CL-MS) epitope-mapping data.
This Zenodo repository contains AlphaFold-predicted structural models of:
This Zenodo repository contains AlphaFold-predicted structural models of:
- the beta (B.1.351) variant RBD, both unbound and in complex with the 1D1 monoclonal antibody,
- the omicron (B.1.1.529) variant RBD, both unbound and in complex with the 1D1 monoclonal antibody, and
- the S1 subunit of the SARS-CoV-2 spike protein.
These models were used as computational structural guides to contextualize residue surface accessibility and the spatial clustering of DEPC-modified residues identified experimentally by CL-MS, particularly when variant-specific high-resolution antigen–antibody complex structures were unavailable. The AlphaFold models were not used as primary evidence for epitope assignment; rather, they assisted in visualizing residue positioning and supporting hypothesis-driven interpretation of solution-phase experimental data.
The AlphaFold models deposited here complement DEPC-based epitope-mapping results and are associated with the manuscript:
“Mass Spectrometry-Based Mapping of Conformational Epitopes on SARS-CoV-2 Antigens Targeted by Monoclonal Antibodies” (unpublished).
All structural models were generated using AlphaFold and are provided to promote transparency, reproducibility, and reuse by the scientific community.
The AlphaFold models deposited here complement DEPC-based epitope-mapping results and are associated with the manuscript:
“Mass Spectrometry-Based Mapping of Conformational Epitopes on SARS-CoV-2 Antigens Targeted by Monoclonal Antibodies” (unpublished).
All structural models were generated using AlphaFold and are provided to promote transparency, reproducibility, and reuse by the scientific community.