User:Catherine Koenigsknecht/Notebook/Experimental Biological Chemistry/2013/01/29: Difference between revisions
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***This merges all the fingerprints into a single fingerprint | ***This merges all the fingerprints into a single fingerprint | ||
*Click File ->Export | *Click File ->Export | ||
**Choose the fingerprint file type (.fp) and assign a name (ex. | **Choose the fingerprint file type (.fp) and assign a name (ex. flavanoid_fingerprints.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 | ***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 | ||
*Restore original names of all structures by clicking Structure -> Change Structure Name Property | |||
**select "Original Title as source property, uncheck the option to store the current name as original title 2 and click ok | |||
**now you may delete the "Flavanoid" column | |||
*Open a command line terminal window -> go to the directory where the fingerprint is: | |||
**type: $SCHRODINGER/utilities/canvasFPCombine -i flavanoid_fingerprints.fp -o flavanoid.modal.fp | |||
3. Add fingerprint to zorro database | |||
*Open in canvas the molecules to be screened (zorro database) | |||
*Add fingerprint to database | |||
**import flavanoid_modal | |||
**click allow duplicate mappings -> click OK | |||
4. Screen Fingerprint | |||
*Applications -> Similarity/Distance screen->select fingerprint | |||
**Tainimoto similarity | |||
**Choose fingerprint column | |||
*After screening select wanted compounds ~15000 | |||
**export | |||
5. Prepare for docking | |||
*Import fingerprint regions to Maestro | |||
*Use ZINC database to download PDB structures of target proteins | |||
*Import PDB structures | |||
*Prepare the proteins: | |||
**Workflows ->protein prep | |||
***Add H+ | |||
***uncheck delete waters | |||
***click preprocess | |||
***Then click refine tab: | |||
****change pH 7.4 | |||
****Optimize: then minimize hydrogens | |||
6. Superimpose Proteins | |||
*Tools ->protein structure alignment | |||
**all->align | |||
**remove H2O and nonpolar H using sidebar | |||
*Use the protein with the higher resolution | |||
*When protein is chosen -> click "show ribbon" to see ribbon structure of protein | |||
7. Docking | |||
*Prepare: remove water molecules | |||
**Duplicate the project | |||
**Click Delete->molecules->manually click H2O | |||
*Make a grid of the docking region | |||
**Application ->glide ->Receptor Grid Generation | |||
***Define ligand: click it | |||
***Click site tab -> center on ligand -> change dock ligands to length 15 angstroms | |||
**Click Start | |||
*Name grid glide-grid_KRM | |||
**check the zorro box | |||
*When run is finished check to redock: | |||
**Isolate ligand | |||
**Click Applications -> ligand docking | |||
***load grid (zip file) ->use project table | |||
***Ensure zorro is selected -> replace 1 with the *-> select 1 test | |||
***Click Start | |||
**Import pv.file | |||
***check new ligand with previous ligand | |||
*Compare flavanoids | |||
**Superimpose flavanoids to ensure similar fit | |||
*Screen database: | |||
**Aplication ->Glide->ligand docking->open file->click start | |||
==Data== | ==Data== |
Revision as of 16:48, 31 January 2013
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Entry titleObjective
Description1. Launching Maestro and Storing Chosen Flavanoid Structures
5. Prepare for docking
6. Superimpose Proteins
7. Docking
Data
NotesThis area is for any observations or conclusions that you would like to note.
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