The data presented in this article are related to the research paper entitled “Anti-inflammatory effect of avenanthramides via NF-κB pathways in C2C12 skeletal muscle cells.” (Kang et al., in press)  This article includes experimental procedures used to analyze the mode of binding between and IkB kinase (IKKβ) and avenanthramides which are a group of phenolic alkaloids found in oats. The protein-ligand docking and the computer simulation method of molecular dynamics (MD) for studying the physical interactions of molecules were performed.
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MD simulations were performed for IKKβ in complex with the structurally solved inhibitors. Each system was solvated in a cubic box with positive TIP3P water  and nutrient ions composed of a solvent buffer zone at the 10 Å edge of the composite. A 100 ns simulation was performed on the docking model using the OPLS-AA 2005 force field under isoelectric isothermal (NPT) conditions at 300 K using DESMOND ver 3.1 (Research DES, Desmond Molecular Dynamics System, NY, USA 2008). The stability of the simulation was evaluated by monitoring the CαRMSD (Root-mean-square deviation of α-carbon) with respect to the minimized starting structure. For IKKβ consisting of the kinase domain (KD), ubiquitin-like domain (ULD) and scaffold/dimerization domain (SDD), CαRMSD was evaluated for the ligand binding KD domain  . This work was supported by INHA UNIVERSITY Research Grant.
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