Crystallography: Changsoo Chan project. Goal: Identify cellulase active site.

cellulales-in-pdb.txt

<<<<<<< Updated upstream

Assay Results

• Carboxymethylcellulose was used a substrate in assay by Matthias Hess. Putatative Endoglucanase.
• Acid-pretreated Miscanthus (real cellulose) showed activity but was not pegged as potential cellobiohydrolases

Endoglucanases in the PDB

• 3qxf (apo)
• 3qxq cellopentaose

Cellopentaose in PDB

• 2eex
• 3a8e
• 3f5k
• 3pl3
• 3qxq
• 3scu
• 4jcw

Surface Screen run

python "/Users/tbinkowski/Box Sync/xScripts/Proteinworks/bin/screen_sdistribution.py" pocket0_atm.pdb 0 "/Users/tbinkowski/Box Sync/xScripts/Proteinworks/bin/surface-library_test_2014-07-23.json" PREFIX

Date: 2014-07-23 13:12

Running: /Users/tbinkowski/Box Sync/xScripts/Proteinworks/bin/screen_sdistribution.py

Machine: tbinkowski2.sbc.anl.gov

CPU count: 24

Query: pocket0_atm.pdb

Library: /Users/tbinkowski/Box Sync/xScripts/Proteinworks/bin/surface-librarytest2014-07-23.json (274962)

Parallel time: 1995.660956

Create surface from the the hexamer interface AG

/Users/tbinkowski/Box\ Sync/xDevelopment/fpocket2/bin/fpocket -f ag.pdb -i 70

The pocket is mirrored at 45 degree (flipped and rotated).

Create the Surface Library from PDB

python /Users/tbinkowski/Documents/Development/Proteinworks/bin/create_library.py -prefix goofy3 -filter_file cellulases-in-pdb.txt 

Surface Screen

python /Users/tbinkowski/Documents/Development/Proteinworks/bin/screen_sdistribution.py apc113179_clean_out/pockets/pocket1_atm.pdb 1 surface-library_goofy3_2014-09-03.json goofy_screen

Stashed changes