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Chloroquine was conjugated to thiolated gold nanoparticles by using EDC/NHS chemistry and the binding was analyzed using optical density measurement and Fourier transform infrared spectroscopy.
For the binding assay, cells were incubated with increasing concentrations of Rh-labeled EGF, and binding was analyzed using flow cytometry.
Annexin V binding was analyzed using the Annexin V-FITC Detection Kit I (Pharmingen, San Diego, CA, USA) according to the manufacturer's instructions.
Binding was analyzed using non-linear regression analysis (GraphPad Prism, Version 3.00 for windows, GraphPad Software (San Diego, CA, USA)).
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Secondary structure and substrate binding were analyzed using CD are in good agreement with the in silico predictions.
Both TUNEL and annexin V binding were analyzed using a flow cytometric analysis on a FACSCalibur cytometer (Becton Dickinson, San Josè, CA, USA).
The performance of the learning methods described above for binding site and CaM binding prediction was analyzed using a number of feature representations which are presented next.
The association between the presence of L1 and AGO2 binding site was analyzed using chi-square test.
To determine whether a gene was also a predicted target of miR-200b and c, the presence of miR-200 family binding sites was analyzed using TargetScan 5.0 (www.targetscan.org [56]).
The ATP binding site was analyzed using the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (http://www.pdb.org) [ 38].
Its binding to DNA was analyzed using isothermal titration calorimetry and UV thermal denaturation, and characterized thermodynamically.
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