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The UsefulChem Project at NERM2006
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The UsefulChem Project at NERM2006


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This is what I presented at NERM in October.

This is what I presented at NERM in October.

Published in: Economy & Finance, Technology

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  • 1. The UsefulChem Project: An Application of Open Source Science in Malaria Research Jean-Claude Bradley PhD, Khalid Mirza, James Giammarco, Dave Strumfels, Lin Cheng
  • 2. Abstract
    • We describe the development of UsefulChem, an open source science project using blogs and wikis to make the scientific process as transparent as possible.  Blogs are used to provide RSS information feeds on experimental details, molecules of interest to the projects, and the thinking process behind the design and evaluation of synthetic strategies. Visitors to the site are able to comment freely on the progress of the experiments as well as offer solutions to any obstacles that may arise.
  • 3. Application
    • This method was applied to a malaria project in which we are synthesizing diketopiperazine derivatives that have been proposed as candidates for inhibition of enyol reductase, an enzyme required for the malarial parasite to propagate.
  • 4. Open science connectivity More info on open source science here
  • 5. UsefulChem Blog
  • 6. UsefulChem Experiments
  • 7. UsefulChem Molecules
  • 8. UsefulChem Writing Partners
  • 9. UsefulChem Wiki
  • 10. CMLRSS feed on Bloglines
  • 11. Automation in UsefulChem
  • 12. Reasons for Change
  • 13. The Story of DOPAL
    • Unusual Rearrangement of 2-Amino-1-Substituted Phenyl-1-Alkanol to 1-Substituted phenyl-2-Alkanone
    • Jack C. Kim*, Myoung-Do Kong, Man-Yong Yoon, Jin Il Park, Soon-Kyu Choi VOLUME 17 NO 2, 1996, 105-106
  • 14. Alteration attempts to Synthesize DOPAL
  • 15. The Successful Synthesis of DOPAL
    • Preparation and properties of p -hydroxyphenylacetaldehyde and 3-methoxy-4-hydroxyphenylacetaldehyde
    • Jay H. Robbins, Archives of Biochemistry and Biophysics, Vol 114 Iss 3, June 1966, 576-584
  • 16. Comparison of NMR data of DOPAL
    • Synthesis of a Bichemically Important Aldehyde 3,4-dihydroxy acetaldehyde
    • Li et al, Bioorganic Chemistry, 26, 45-50 1998
    3,4-Dihyroxystyrene Dimers, Inducers of Larval Metamorphosis of Ascidians from a Marine Sponge Jaspis sp Tsukamoto et al, Tetrahedron, Vol 50, No 48, 13583-13592, 1994
  • 17. Comparison of NMR data of DOPAL
  • 18. Debugging the Ugi
    • Solution Phase Synthesis of Diketopiperazine Libraries Via the Ugi Reaction: Novel Application of Armstrong’s Covertable Isonitrile
    • Christopher Hulme*, Matthew M Morrisette, Francis A Volz, and Christopher J. Burns, Tetrahedron Letters, 39 (1998), 1113-1116
  • 19. Debugging the Ugi
  • 20. Progress
  • 21. Comments on UsefulChem Blogs
  • 22. Next Steps
    • Incorporate our molecules into Emolecules to enable substructure searching
    • Custom CMLRSS feeds (e.g. only new commercial sources found)
    • Get spectra in JCAMP format
    • Extend our collaboration with other chemists (e.g. docking data)
    • Get our anti-malarials made and tested
  • 23. References