Supplementary Figure 7: Hybrid MaSIF-search/MaSIF-site protocol to identify true binders against PD-L1.
From: Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
The target site is first predicted using MaSIF-site. Then a database of nearly 11,000 proteins is scanned, all patches with a MaSIF-site score > 0.9 and with a descriptor distance less than 1.7 are selected for alignments. Top candidates are matched using RANSAC, and reranked using the descriptor distance of all aligned points (described in Methods). The top predicted complex was the PD-L1:Mouse PD1 (PDB ID 3BIK), ranked #1 with an RMSD of 0.6 Å (shown here in pale orange). The PD-L1:Human PD1 (PDB ID 4ZQK), was ranked #8 with an RMSD of 0.3 Å. Both are shown overlaid over the initial complex (PDB ID 4ZQK). The entire runtime protocol took approximately 26 minutes (excluding descriptor precomputation time).
