AbDb parsing- BP3 procedure #2
Description
See https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4497
We first identified crystal structures from the Protein Data Bank deposited before September 29, 2021 that contain at least one complete antibody, and at least one non-antibody (antigen) protein chain.4 This was done using existing hidden markov model (HMM) profiles developed in-house.14 We only included crystal structures with a resolution lower than 3 Å and R-factor lower than 0.3. On both datasets, we identified epitope residues using the same approach adopted in our previous paper.11 On each antigen chain, we labeled every residue that had at least one heavy atom (main-chain or side-chain) at a distance of <4 Å to any heavy atom belonging to residues in antibody chains of the same crystal structure as an epitope residue. We only retained antigen chains with at least one epitope residue and with a minimum sequence length of 39. Epitope residues for antigens which were 100% identical in sequence were merged and only one antigen entry included. Missing residues were not included as part of the epitope annotated antigen chains. After these steps, we obtained a total of 1,466 antigens for the updated BP3 dataset.
Adapt this procedure