Author: Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou
Title: Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening Document date: 2018_9_16
ID: 40pe21lm_22
Snippet: We use a previously benchmarked GRAMM-X 15 to obtain the initial PFN1-P10 binding structures to determine the binding modes. The rigid docking algorithm is suitable for PFN1-P10 based on the root mean square displacements (RMSDs) of PFN1 and P10 during the MD simulations (see below). Figure 1 shows the top 10 docked protein-protein structures ranked by the prediction scores from mode1 to mode10 (most stable to least stable) as well as the crystal.....
Document: We use a previously benchmarked GRAMM-X 15 to obtain the initial PFN1-P10 binding structures to determine the binding modes. The rigid docking algorithm is suitable for PFN1-P10 based on the root mean square displacements (RMSDs) of PFN1 and P10 during the MD simulations (see below). Figure 1 shows the top 10 docked protein-protein structures ranked by the prediction scores from mode1 to mode10 (most stable to least stable) as well as the crystal structure mode11 (PDB ID: 1AWI) added for completeness. Note that the co-crystal structure binding mode was predicted by GRAMM-X (mode9).
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