Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening

Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/418830 doi: bioRxiv preprint reliable way of identifying the binding mode with the lowest binding free energy, as shown by a correlation coefficient (R 2 ) as high as 0.7 (from the rank order correlation). We argue that even though the rigidity of both PFN1 and P10 may prevent us from generalizing the conclusion, by applying some constraints, SMD can be used to quickly screen the stable binding modes found from docking programs. With a clearer understanding of the advantages and disadvantages of various PPI techniques tested, we hope to expand them with a fast binding-mode-screening method to study PPI pairs found in the human interactome network 55 .