PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models

BMC Bioinformatics

Table 2 Performance comparison with other methods on binary complex dataset

Method	Test set 1	Test set 2
Method	PCC\(\uparrow\)	PCC\(\uparrow\)
\({\hbox {Rosetta-InterfaceAnalyze}}^1\)	0.482	0.054
\({\hbox {Foldx-AnalyseComplex}}^2\)	0.076	\(-\) 0.159
\({\hbox {ColabFold-iPAE}}^3\)	0.588	0.156
ours	0.708	0.633

\(^{1}\)The dG_separated score generated by RosettaFold’s InterfaceAnalyzer to indicate binding affinity. Prior to this, the PDB files were processed using relax and jd_score2
\(^{2}\)The Interaction Energy score generated by FoldX’s AnalyseComplex module to indicate binding affinity
\(^{3}\)The iPAE yielded by ColabFold to indicate binding affinity

ISSN: 1471-2105