Computational protocol: Computationally driven identification of antibody epitopes

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Protocol publication

[…] Thirty-three Ab-Ag pairs with complex structures solved by X-ray crystallography () were selected from SAbDab () according to the following criteria: pairwise Ab sequence identity <70%, pairwise Ag sequence identity <70%, resolution <3 Å, single-chained, and >50 and <300 residues in length. Structures missing any backbone atoms were excluded.In order to consider practical applications in a realistic setting, all Ab structures were homology modeled in a manner established to simulate ‘hard-to-model’ situations, for which template sequence identity is less than 90% (). Abs were modeled using the PIGS webserver with restricted sequence identity templates (<80% to the target) followed by side chain energy minimization using Tinker as described above. The quality of the Ab models was extremely accurate (), both overall (TM-score: 0.95) and for CDRs (<2 Å for CDR-H3 and sub-Angstrom for others), consistent with a report on CDR-H3 modeling quality ().Ag targets were either crystal structures from the bound complexes, or homology models built by SWISS-MODEL () with default parameters applied to templates. Again, in order to represent realistic application, templates were selected to keep sequence identity low. When possible, the sequence identity was restricted to be less than 50%, but for nine cases had to be increased due to lack of any targets at that cut off. The resulting average template sequence identity was 46%, ranging from 23% to 99% ().Experimentally identified epitopes were obtained from the IEDB ().For the multiple Ab test set, 12 Abs were modeled from sequences () as described above. PDB code 4E9O:X was used for the vaccinia D8 structure. FREAD identified 2AZW:A 87–91 (SNHRQ) as the best match for the missing loop from 207 to 209 (SNHEG), and this structural fragment was grafted into the model as described above. […]

Pipeline specifications

Software tools TM-Score, SWISS-MODEL, FREAD
Databases IEDB
Applications Small-angle scattering, Protein structure analysis
Chemicals Amino Acids