Position dEpendent Antibody Rotamer Swapper
- PEARS is a side chain prediction method that uses the IMGT position-dependent distribution of rotamers.
- The heavy and light chains are initially numbered using the IMGT numbering scheme via ANARCI.
- PEARS initially builds the disulphide bridges of the antibody chains.
- PEARS then searches for position-amino acid combinations (i.e. side chain types) that have a unimodal χ1 angle. At specific locations, some amino acids tend to have one χ1 angle.
- Once these unimodal side chain types are predicted, PEARS predicts the remaining side chains using dead-end elimination and graph decomposition.
- PEARS typically requires less than 10 seconds to complete the side chain prediction process.
- An example of the output produced by PEARS can be seen here. The following output files can be downloaded:
- IMGT-renumbered structure - the input structure in the IMGT numbering scheme
- PDB-numbered structure - the input structure with the original numbering, but with the new side chains
- Mapping files - text files that correlate residue numbers from the input PDB file into the IMGT numbering.
For a full description of the software, or if you use it, please refer to: Leem J, et al. Antibody side chain conformations are position‐dependent. Proteins. (2018)
