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To find possible differences between covalent and non-covalent binding approaches, we performed a multiparameter flow cytometry assay (Additional file 1: Figure S3A D).
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In addition to this candidate approach, we performed an unbiased proteomics screen for PTPδ binding proteins.
As first approach we performed the microfocus formation assay.
To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson Boltzmann surface area (PBSA) and other approaches.
To test the binding specificities, we performed ITC to measure the equilibrium disassociation constants (Kd).
To demonstrate that this binding is specific, we performed a competition binding experiment.
To assess the impact of the T109M mutation on PFN1 binding to PLP, we performed molecular-dynamic simulations.
To determine whether β-casein 197 had DNA-binding capabilities, we performed a gel retardation assay.
To determine whether GAG-binding capacity is required for receptor binding and cell activation, we performed competition radioligand binding and calcium mobilization experiments using one of the non-heparin-binding mutants, R46A.
To determine whether the binding region of anti-CXCR4 antibody corresponded to CXCR4-binding domain for SU, we performed competition binding assay in 3201 cells.
To explore the TF binding motifs inside TEs, we performed de novo motif discovery.
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