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. 2022 May 10;13:878762. doi: 10.3389/fimmu.2022.878762

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Copyright © 2022 Marzella, Parizi, Tilborg, Renaud, Sybrandi, Buzatu, Rademaker, ‘t Hoen and Xue

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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PANDORA’s case studies on with non-canonical cases. The images are oriented to present the most representative view of the difference between models and target. (A) PANDORA produced better models than using canonical anchor positions in terms of backbone L-RMSD of cases. (B) A typical case (target PDB ID: 1DUY, template PDB ID: 1AO7 in Red, peptide=LFGYPVYV) with non-canonical anchor positions Blue with (actual anchors: P1 and P9(Ω). (C) Case study on the 10-mer from PDB structure 3BEW (Red). L-RMSD with default settings: 2.02 Å (Yellow); L-RMSD using secondary structure restraints: 0.80 Å (Blue). (D) Case study on the 15-mer from PDB structure 4U6Y (Red). L-RMSD with default settings: 3.32 Å (Yellow); L-RMSD using secondary structure restraints: 1.50 Å (Blue).