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Molecular Docking

KG K. R. D. Sagara N. S. Gurusinghe
AM Aanchal Mishra
SM Seema Mishra
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Molecular docking studies using protein (energy minimized), ATP and EGCG inhibitor were done using AutoDock Vina18 protein-ligand docking tool within the PyRx 0.8 virtual screening tool. Docked structures with ATP were compared with crystal structures to provide benchmarking. Docking parameters were selected by comparing these docked structures to the original crystallographic structure (PDB ID: 5E84) and finding out similar binding modes. On the basis of this result, modified parameters for Vina search space were as follows: x-centering: −0.7101, y-centering: 33.96 and z-centering: −28.62. The free-energy scoring function in AutoDock Vina uses information from both knowledge-based potentials and empirical scoring functions, and Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for local optimization. Iterated Local Search optimizer is used for global optimization. ATP and EGCG were docked into ATPase domain (NBD) of full-length GRP78 protein.

Copyright and License information: The Author(s) ©2018
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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