A comprehensive antigen-antibody complex database unlocking insights into interaction interface
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, China
- School of Healthcare Technology, Chengdu Neusoft University, China
Figures
Figure 1
Antigen-Antibody Complex Database (AACDB) statistics.
(A) Antibody fragment distribution in the database. (B) The number of antibody-antigen complexes released in different years (unique PDBID). (C) Organismal distribution of antibody entries. Statistical cutoff date: May 30, 2024. Fab: antigen binding fragment; Fv: variable fragment; scFv: single chain variable fragment; VHH: Variable domain of heavy chain of heavy chain antibody; sdAb: single domain antibody.
Figure 2
The Antigen-Antibody Complex Database (AACDB) browse and search page.
This example demonstrates the use of the keyword ‘Lysozyme’ in the ‘Protein’ column, showcasing the search functionality of the AACDB database. The search results display an antigen related to lysozyme.
Figure 3
The details page of entries, taking ‘1BJ1’ as an example.
(A) Structure visualization window. The molecular structure is displayed with distinct color-coding for clarity: each chain is represented by a unique color, facilitating easy identification. The epitope is highlighted in blue, while the paratope is marked in green (B) Entry meta information. (C) Sequence and mutation information. (D) Interacting residues details based on solvent accessible surface area (SASA) and atom distance methods. (E) The download hyperlinks of a single entry.
Figure 4
The Antigen-Antibody Complex Database (AACDB) framework integrates standardized metadata, interface annotation, and antigen-drug target relationships for comprehensive antigen-antibody complex analysis.
Figure 5
Data processing algorithm pipeline of Antigen-Antibody Complex Database (AACDB).
Figure 6
Examples of Protein Data Bank (PDB) file splitting under different situations.
(A) 1AHW contains two copies of the same antigen and the same antibody. (B) In 6OGE, two different antibodies bind to distinct epitopes of the same antigen. (C) In 3BQU, an anti-idiotypic antibody binds exclusively to a single chain of the antibody.
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A comprehensive antigen-antibody complex database unlocking insights into interaction interface
eLife 14:RP104934.
https://doi.org/10.7554/eLife.104934.3
