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. 2018 Nov 19;8:16985. doi: 10.1038/s41598-018-35069-0

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© 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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Molecular dynamics, molecular modeling and structural perturbation analysis of CD44v6 by selected potential drug compound. (a) RMSD trajectory analysis of the modeled CD44v6 structure in bound form with HA and Silibinin during 50 ns long MD simulations. Notes: Duration of MD simulations scaled on X-axis and Y-axis on the left side represents the RMSD deviation of protein structure in Å. Y-axis on the right side represents the HA ligand RMSD trajectory in their respective binding pockets. (b) RMSF analysis of the modeled CD44v6 structure in bound form with HA and Silibinin during 50 ns long MD simulations. The highlighted regions (red) is depicting ligand induced internal residual fluctuations in CD44v6 structure captured during MD simulation process. (c) 3D representation of the superimposed complexes of CD44v6 bound to HA (green) and Silibinin (pink) respectively demonstrating ligand induced conformational change in the structure of CD44v6 protein. (d) Difference in H-bond interaction profile of CD44v6 with HA and Silibinin before and after MD simulation process.