Below is a video of two 400ns long all-atom classical molecular dynamics trajectories of Rap:Raf complex.
The "ice blue" and "orange" tubes are Rap:Raf complex with phosphorylated Serine at 39th site in Rap chain. The red/blue colored region of the tube is the Switch-I. For a context see this article:
https://www.steemstem.io/#!/@dexterdev/why-ser11-site-was-chosen-as-the-phosphorylation-site-a-frequent-question-which-we-encounter-regarding-our-work
Did you make this from your own experimental data? If so what program? It’s been a while since I’ve dealt with protein structure, but the modeling programs have always been fascinating.
The initial structure is downloaded from protein data bank(id: 1C1Y). We used this structure to perform molecular dynamics.
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