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Structure Investigation of Fam20C, A Golgi Casein Kinase

Structure Investigation of Fam20C, A Golgi Casein Kinase. Sharon Grubner National Taiwan University Third Weekly report – July 10 th , 2013. Progress. First free dynamics simulation was completed today! Learned how to use RMSD Visualizer in VMD Select specific ranges of residues

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Structure Investigation of Fam20C, A Golgi Casein Kinase

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  1. Structure Investigation of Fam20C, A Golgi Casein Kinase Sharon Grubner National Taiwan University Third Weekly report – July 10th, 2013

  2. Progress • First free dynamics simulation was completed today! • Learned how to use RMSD Visualizer in VMD • Select specific ranges of residues • Edit and analyze RMSD plots of bond interactions • Learned how to use VolMap Tool in VMD • Looking at the percentage of water molecules present inside the ATP binding pocket • Clustering • Learned about clustering • Practiced preparing the trajectory files and using GROMACS clustering- still having issues, will continue working on it next week • My progress is being updated on a daily basis and shared with my mentors on Evernote.

  3. Goals for Next Week Repeat and implement some of the analysis tools I have learned how to use in the past couple of weeks, on the first final free dynamics simulation which was just completed. • Watch the motion of various loops within Fam20C structure (K171-178, A300-306) • Quantitative analysis – RMSD Visualizer Tool • Qualitative analysis- watch trajectory and draw conclusions for drug discovery purposes • Analyze the distance between alpha carbons to analyze larger motions of P-loop • Start to measure and plot distances of salt bridge interactions between certain residues, throughout the simulation • Fix clustering tool errors

  4. Culture Had a great day with good friends at Jiufen

  5. Gold Museum at Jiufen- a town used as inspiration for the movie Spirited Away Longshan temple Jiufen famous desert- sweet potato and yam dumplings with brown-sugar and ice

  6. Acknowledgments • UCSD (University of California San Diego) • Dr. RommieAmaro • Dr. Gabriele Wienhausen • Dr. Peter Arzberger • Teri Simas • NTU (National Taiwan University) • Dr. Jung-HsinLin • Julia Brown Undergraduate Research Scholarship

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