SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network
Fig 5
An illustrative example to highlight the dense local contacts accounted by SPIN-CGNN for improving fixed backbone design.
(A) The neighbors for residue 10 (yellow) in PDB 2AUV chain A, which has the greatest number of neighbors determined by CGraph12 (magenta). (B) The AlphaFold2-predicted structure of sequence designed by SPIN-CGNN (magenta), aligned on the native PDB structure (green). (C) The neighbors determined by KNN-30 (cyan) for the same protein. (D) The corresponding AlphaFold2-predicted structure of sequence designed by PiFold (cyan).