Extended Data Fig. 3: The docking performance of RAPiDock on SHP2.
From: Protein–peptide docking with a rational and accurate diffusion generative model
(a) The sequences of 5X7B (N-SH2 domain of SHP2) and 5X94 (C-SH2 domain of SHP2). (b) left: The overlay of protein residues of 5X7B and 5X94. In SH2 domains, two structural regions determine the PpI: (1) the phosphotyrosine binding site, a groove-like structure formed by the αA helix, βB/βC/βD strands, and BC loop, and (2) the specificity pocket, which is a relatively large hydrophobic pocket mainly delimited by residues of αB helix, βD strand, and BG and EF loops. The phosphotyrosine binding site is relatively conserved, whereas the specificity pocket is more flexible; right: the peptides of 5X7B and 5X94 share a common 7-residue sequence PIpYATID. Given the pTyr residue serving as a reference, the residues from −2 to +3 align well in the pocket. The residues at +4 of the peptides exhibit obvious deviation, influenced by structural differences in the protein near the BG loop. Specifically, the proteins of 5X7B and 5X94 are colored green and yellow, respectively, while their peptides are colored white and gray, respectively. (c) Top-ranked peptide conformation generated by RAPiDock for 5X7B. (d) Top- ranked peptide conformation generated by RAPiDock for 5X94. The peptide conformations generated by RAPiDock are colored coral red.
