User:Catherine Koenigsknecht/Notebook/Experimental Biological Chemistry/2013/01/29: Difference between revisions

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*Optimize molecule to lower energy state
*Optimize molecule to lower energy state
**Use Impact Energy Minimizer under Application: change host to zorro
**Use Impact Energy Minimizer under Application: change host to zorro
**Export Structures
2. Generate Fingerprints
*Launch Canvas from terminal:
**select directory from terminal: press F5: type $canvas
*Import molecule structures
**Applications ->binary fingerprints -> molprint2D
**Run Program
*Click Edit -> Add Column and name column (ex. Flavanoids)
**Right-click header of new column and choose "Set Property Value"
***Type in a temporary name for the set of reference compounds in the modal fingerprint (ex. modal row fingerprint row)
***Click OK
*Click Structure ->Change Structure Name Property
**Select "Flavanoid" as the source property  and ensure "Store current as new property" is selected.
***This merges all the fingerprints into a single fingerprint
*Click File ->Export
**Choose the fingerprint file type (.fp) and assign a name (ex. flavanoid.fp)
***In the next Export Options dialog which opens, ensure the desired fingerprint is selected, remove all properties from the "selected properties" list, uncheck the option to Export Canvas UIDs and click OK


==Data==
==Data==

Revision as of 16:25, 31 January 2013

Biomaterials Design Lab <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Entry title

Objective

  1. Learn how to use Maestro Software
  2. Identify fingerprint zone of flavonoids: Myricetin, Kaempferol, and Quericetin
  3. Perform docking of compounds to identify similar compounds

Description

1. Launching Maestro and Storing Chosen Flavanoid Structures

  • Launch Maestro from terminal:
    • select directory from terminal: press F5: type $maestro
  • Draw Structures on Maestro
    • Edit -> build -> fragments: when finished create project
    • Workspace ->Create Project
  • Optimize molecule to lower energy state
    • Use Impact Energy Minimizer under Application: change host to zorro
    • Export Structures


2. Generate Fingerprints

  • Launch Canvas from terminal:
    • select directory from terminal: press F5: type $canvas
  • Import molecule structures
    • Applications ->binary fingerprints -> molprint2D
    • Run Program
  • Click Edit -> Add Column and name column (ex. Flavanoids)
    • Right-click header of new column and choose "Set Property Value"
      • Type in a temporary name for the set of reference compounds in the modal fingerprint (ex. modal row fingerprint row)
      • Click OK
  • Click Structure ->Change Structure Name Property
    • Select "Flavanoid" as the source property and ensure "Store current as new property" is selected.
      • This merges all the fingerprints into a single fingerprint
  • Click File ->Export
    • Choose the fingerprint file type (.fp) and assign a name (ex. flavanoid.fp)
      • In the next Export Options dialog which opens, ensure the desired fingerprint is selected, remove all properties from the "selected properties" list, uncheck the option to Export Canvas UIDs and click OK

Data

  • Add data and results here...

Notes

This area is for any observations or conclusions that you would like to note.


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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