Abstract
To study and compare the simulation methods on the different scoring functions to analyze the consistency of the Docking score between the aptamers and protein. Thrombin is well characterized and has been studied with the thrombin binding aptamer (TBA) and mutated TBA sequences in a previous report, which finds three representative aptamers have best, medium, and worst binding interactions with thrombin. Discovery Studio 3.5 is a useful modeling and simulation software. The ZDOCK in this package incorporates a simple and novel scoring function: Pairwise Shape Complementarity. By using ZDOCK, we also can evaluate the differences in the binding ability between the interactions of the thrombin and aptamers. Basically, our results are consistent with the previous report. From this study, we make sure that the ZDOCK can provide reliable results and able be used as an alternative method in performing in silico selection of aptamer.
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Acknowledgments
The authors gratefully acknowledge the financial support provided by Asia University (Taiwan) under contract number 101-asia-23.
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Kumar, J.V., Chen, WY., Tsai, J.J., Hu, WP. (2013). Molecular Simulation Methods for Selecting Thrombin-Binding Aptamers. In: Park, J.J., Barolli, L., Xhafa, F., Jeong, H.Y. (eds) Information Technology Convergence. Lecture Notes in Electrical Engineering, vol 253. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6996-0_78
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DOI: https://doi.org/10.1007/978-94-007-6996-0_78
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