uPA


re-docking of ligands with known x-ray structure conformation into uPA

excel sheets: ~/report/zope/2006-01/results_docking-20A.xls

ranked: http://projects.villa-bosch.de/mcm/projects/tassfun/reports/2006-01/results_docking-20A-ranked.html
file:///home/henricsn/report/zope/2006-01/results_docking-20A-ranked.html

rescaled:
http://projects.villa-bosch.de/mcm/projects/tassfun/reports/2006-01/results_docking-20A-rescaled-LV5.html
file:///home/henricsn/report/zope/2006-01/results_docking-20A-rescaled-LV5.html

docked ligands
http://projects.villa-bosch.de/mcm/projects/tassfun/reports/2006-01/testset-rankedA.html
http://projects.villa-bosch.de/mcm/projects/tassfun/reports/2006-01/testset-rankedP.html


docking of ligands into uPA model
known Ki of ligands, (mostly) unknown x-ray structures

docking-testset (model5-cut.pdb)
/work/priamos/stefan/home/henricsn/combine2go/data/urokinase/docking-testset/

GOLD v3.0.1
radius = 22
floodfill_atom_no = 3559
protein_datafile = model5-cut.pdb
ligand_data_file uPA_191205_3D.sdf 10
directory = /work/priamos/stefan/home/henricsn/combine2go/data/urokinase/docking-testset
goldscore

docking solution: uPA_191205_3D.sdf
golpe: uPA_191205_3D.dat
excel: ~/report/zope/2006-02/docking-testset_model5_model2.xls (sheet 1 'model5')

docking-testset-model2 (model2-cut.pdb)
/work/priamos/stefan/home/henricsn/combine2go/data/urokinase/docking-testset2/

GOLD v3.0.1
radius = 22
floodfill_atom_no = 3559
protein_datafile = model2-cut.pdb
ligand_data_file uPA_191205_3D.sdf 10
directory = /work/priamos/stefan/home/henricsn/combine2go/data/urokinase/docking-testset2
goldscore

excel: ~/report/zope/2006-02/docking-testset_model5_model2.xls (sheet 2 'model2')
nonbinders
/work/priamos/stefan/home/henricsn/combine2go/data/urokinase/nonbinders
PLATED_1-50.sdf

GOLD v3.0.1
radius = 22
floodfill_atom_no = 3559
protein_datafile = model5-cut.pdb
ligand_data_file PLATED_1_16.sdf 10
ligand_data_file PLATED_18_50.sdf 10
directory = /work/priamos/stefan/home/henricsn/combine2go/data/urokinase/nonbinders
goldscore

golpe: PLATED_1_16.dat PLATED_18_50.dat
excel: ~/report/zope/2006-02/uPA-nonbinders/nonbinders-prediction.xls (html)

trypsin

~/combine2go/data/trypsin/

~/combine2go/data/trypsin/mod17_151205/golpe-bos/trypsin-model.dat
trypsin model


ligands of Klebe/Stuerzebecher/Boehm docked into trypsin model
~/combine2go/data/trypsin/dock_klebe/
http://projects.villa-bosch.de/mcm/projects/tassfun/reports/2005-12/docking_klebe_ligands.html
(first docking trails for trypsin model)

GOLD v3.0
radius = 10
floodfill_atom_no = 2539
protein_datafile = trypsin-model.minbres.pdb
ligand_data_file klebe_151205_3D.sdf 10
directory = /home/henricsn/combine2go/data/trypsin/dock_klebe/
goldscore

Radius for active site was too small!

The performed minimizations and interaction energie calculations are not useful!
min/ (date 21.12.05)
min-all/ (date 10.01.06)
min-all-neu/ (date 13.01.06)
redocking of ligands, which were used for model building of trypsin (mod17_151205/)
~/combine2go/data/trypsin/redocked_mod17_151205/

GOLD v3.0
radius = 20
floodfill_atom_no = 2539
protein_datafile = trypsin-model.minbres.pdb
ligand_data_file PDB_trypsin_191205_3D.sdf 10
directory = /home/henricsn/combine2go/data/trypsin/redocked_mod17_151205
goldscore

docking solutions (SDF)
golpe: PDB_trypsin_191205_3D.dat

trypsin-redocked_mod17_151205.xls
sheet:
88 ligands of Klebe/Stuerzebecher/Boehm dataset docked into trypsin model
without any xray structures; ligands not in training set

/scratch/priamos/stefan/trypsin_dock_klebe_230106/

GOLD v3.0.1
radius = 22
floodfill_atom_no = 2539
protein_datafile = trypsin-model.minbres.pdb
ligand_data_file klebe_151205_3D.sdf 10
directory = /exports/scratch/stefan/trypsin_dock_klebe_230106
goldscore

docking solutions (SDF)
golpe: klebe_151205_3D.dat

predicted values:
trypsin-mod17_151205-dock-klebe-22A_230106-best-ranked
~/report/zope/2006-01/trypsing-mod17_151205-dock-klebe-22A_230106.xls
sheets:

thrombin

docking of ligands into thrombin model (without sodium of active site)
/home/henricsn/combine2go/data/thrombin/docking/

excel: ~/report/zope/2006-02/thrombin/docking-thrombin.xls
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