User:Catherine Koenigsknecht/Notebook/Experimental Biological Chemistry/2013/02/05

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#01668680 Sigma 696366|ALDRICH
#01668680 Sigma 696366|ALDRICH
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==Data==
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==Notes==
==Notes==

Revision as of 15:32, 5 February 2013

Biomaterials Design Lab Main project page
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Entry title

Analysis of Docking Screen for ADA

Objective

  1. View docking score results
  2. Compare docking scores to known flavonoids
  3. Identify possible alternatives to known flavonoids using docking scores
  4. Locate chosen alternative compounds and purchase for additional testing

Description

  • View docking scores of screened compounds:
  1. Open Maestro
  2. Project->import structures: open grid_grid_SP_1500Flavanoids.pv
  3. Project Table: View docking scores (more negative docking score = better docking


  • Identify top score compound structures: (using project table)
    • Look at H bonds and fit of structure
    • Look at compounds with flavonoid similarity
      • sort by fpscreen_1 on table (larger the score the closer to flavanoid)
        • identify flavonoid structures by viewing compounds
  • High Flavonoid Scores
  1. 04098600: -5.485 (Indofine, Sequoia, TimTec, Ambinter)
  2. 03881558: -4.625 (
  3. 06536276: -4.296
  4. 18185774: -6.471
  5. 06095498: -5.272
  6. 03775158: -5.843
  7. 13520048: -5.785
  8. 14644239: -5.443
  9. 48057104: -5.777
  10. 00057756: -5.368
  11. 14644152: -5.836


  • High Docking Scores
  1. 13481458: -9.57
  2. 08701835: -9.511
  3. 66442578: -9.452
  4. 01705123: -9.364
  5. 03145514: -9.358
  6. 08702204: -9.296
  7. 01668680: -9.232
  8. 14984581: -9.231
  9. 14984586: -9.212
  10. 03608745: -9.171
  11. 05886403: -9.168
  12. 65349920: -9.149
  13. 00189726: -9.08
  14. 00057725: -9.051
  15. 00845395: -9.038
  16. 02386823: -9.017
  • Input ID numbers into Zinc database:
  1. View Vendors and avaliability
  • Choose COmpounds to Order and test:

ZINC# Ambinter Ref #

  1. 4098600 Amb18511408
  2. 3881558 Amb18511704
  3. 18185774 Amb18511398
  4. 06095498 Amb18511625
  5. 13520048 Amb18511697
  6. 14644239 Amb19928292
  7. 48057104 Amb21928522
  8. 00057756 Amb20665183
  9. 14644152 Amb19928577
  10. 13481458 Amb17201778
  11. 03145514 Amb1196791
  12. 00189726 Amb1334505
  13. 00057725 Amb1151325
  14. 08701835 Asischem Building Blocks A63086
  15. 08702204 Asischem Building Blocks C31214
  16. 01668680 Sigma 696366|ALDRICH


Notes

Docking Scores for the flavanoids:

Myricetin: -6.237

Kaempferol: -6.067

Quercetin: -5.905


Use categories like tags. Change the "Course" category to the one corresponding to your course. The "Miscellaneous" tag can be used for particular experiments, as instructed by your professor. Please be sure to change or delete this tag as required so that the categories remain well organized.



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