Difference between revisions of "DOCK 3.7 tart"

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Tarting refers to the polarization of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generaly one would redefine the partial charges distribution of a specific amino acid, and then use this modified residue when calculating the electrostatic potential for the receptor. Below is a step by step example:
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Tarting refers to the polarization of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generally one would redefine the partial charges distribution of a specific amino acid, and then use this modified residue when calculating the electrostatic potential for the receptor. Below is a step by step example:
 
* Let's say you ran docking against RSK2, so you have a docking directory that looks like: rec.pdb, xtal-lig.pdb, dockfiles, working, INDOCK
 
* Let's say you ran docking against RSK2, so you have a docking directory that looks like: rec.pdb, xtal-lig.pdb, dockfiles, working, INDOCK
 
* Make a new dir e.g. RSK2-tart, and copy some input files into it:  
 
* Make a new dir e.g. RSK2-tart, and copy some input files into it:  
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** cp RSK2/working/rec.crg.pdb RSK2-tart/working
 
** cp RSK2/working/rec.crg.pdb RSK2-tart/working
 
** cp RSK2/working/prot.table.ambcrg.ambH RSK2/working/amb.crg.oxt RSK2-tart
 
** cp RSK2/working/prot.table.ambcrg.ambH RSK2/working/amb.crg.oxt RSK2-tart
* Now edit the files to represent your tweeked polarization. Let's say we want to polarize the backbone of MET496 (In this case the kinase hinge region) by +-0.4
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* Now edit the files to represent your tweaked polarization. Let's say we want to polarize the backbone of MET496 (In this case the kinase hinge region) by +-0.4
 
** Edit RSK2-tart/working/rec.crg.pdb to rename "MET A 496" to "MEU A 496"
 
** Edit RSK2-tart/working/rec.crg.pdb to rename "MET A 496" to "MEU A 496"
 
** Edit RSK2-tart/prot.table.ambcrg.ambH to add a MEU amino acid. You can copy the block for MET and rename it to MEU, to polarize the backbone, change the partial charge of the backbone amide proton by +0.4 (i.e. "H    MEU        0.648" instead of "H    MEU        0.248") lower the backbone carbonyl oxygen by the same quantity ("O    MEU      -0.500" to "O    MEU      -0.900")
 
** Edit RSK2-tart/prot.table.ambcrg.ambH to add a MEU amino acid. You can copy the block for MET and rename it to MEU, to polarize the backbone, change the partial charge of the backbone amide proton by +0.4 (i.e. "H    MEU        0.648" instead of "H    MEU        0.248") lower the backbone carbonyl oxygen by the same quantity ("O    MEU      -0.500" to "O    MEU      -0.900")
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** $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-art/prot.table.ambcrg.ambH
 
** $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-art/prot.table.ambcrg.ambH
  
When the prepartaion is done, your protein should be "Tarted". You can proceed to docking.
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When the preparation is done, your protein should be "Tarted". You can proceed to docking.

Revision as of 16:56, 23 April 2015

Tarting refers to the polarization of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generally one would redefine the partial charges distribution of a specific amino acid, and then use this modified residue when calculating the electrostatic potential for the receptor. Below is a step by step example:

  • Let's say you ran docking against RSK2, so you have a docking directory that looks like: rec.pdb, xtal-lig.pdb, dockfiles, working, INDOCK
  • Make a new dir e.g. RSK2-tart, and copy some input files into it:
    • mkdir RSK2-tart
    • cp RSK2/rec.crg RSK2/xtal-lig.pdb RSK2-tart
    • mkdir -p RSK2-tart/working
    • cp RSK2/working/rec.crg.pdb RSK2-tart/working
    • cp RSK2/working/prot.table.ambcrg.ambH RSK2/working/amb.crg.oxt RSK2-tart
  • Now edit the files to represent your tweaked polarization. Let's say we want to polarize the backbone of MET496 (In this case the kinase hinge region) by +-0.4
    • Edit RSK2-tart/working/rec.crg.pdb to rename "MET A 496" to "MEU A 496"
    • Edit RSK2-tart/prot.table.ambcrg.ambH to add a MEU amino acid. You can copy the block for MET and rename it to MEU, to polarize the backbone, change the partial charge of the backbone amide proton by +0.4 (i.e. "H MEU 0.648" instead of "H MEU 0.248") lower the backbone carbonyl oxygen by the same quantity ("O MEU -0.500" to "O MEU -0.900")
    • Edit RSK2-tart/amb.crg.oxt to reflect the same changes
  • Now all that's left is to run the protein preparation script (blastermaster.py) with the modified parameter files, and without re-protonating the protein:
    • $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-art/prot.table.ambcrg.ambH

When the preparation is done, your protein should be "Tarted". You can proceed to docking.