Protein Target Preparation Updated - Revision history

Rstein: /* Running Blastermaster */

2019-10-10T18:59:39Z

Running Blastermaster

← Older revision		Revision as of 18:59, 10 October 2019
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	rec.pdb		rec.pdb
	xtal-lig.pdb		xtal-lig.pdb

			A useful way to get these files is to run Trent's be_balsti wrapper on your PDB. If you have the file, 1YPE.pdb, in your current directory, run the following command:

			csh /mnt/nfs/home/rstein/zzz.scripts/DOCK_prep_scripts/0001.be_balsti_py.csh 1YPE

			This will create a new directory "1YPE" with rec.pdb and xtal-lig.pdb files.

	Before running blastermaster, consider the following:		Before running blastermaster, consider the following:
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	Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.		Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.
	Are all residues built in your structure? Blastermaster will not give you an error if they are not.		Are all residues built in your structure? Blastermaster will not give you an error if they are not.
			Are there multiple conformations for any residues? Running 0001.be_balsti_py.csh should take conformation A if there are multiple conformations
	Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are renamed to "CYX" in your rec.crg.pdb file after blastermaster runs.		Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are renamed to "CYX" in your rec.crg.pdb file after blastermaster runs.
			Are there ions in your structure? Should they be?

	If you have missing residues, Schrodinger can be used to build them:		If you have missing residues, Schrodinger can be used to build them:

Rstein: /* Running Blastermaster */

2019-10-04T02:10:44Z

Running Blastermaster

← Older revision		Revision as of 02:10, 4 October 2019
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	Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.		Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.
	Are all residues built in your structure? Blastermaster will not give you an error if they are not.		Are all residues built in your structure? Blastermaster will not give you an error if they are not.
	Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are renamed to "CYX" after blastermaster runs.		Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are renamed to "CYX" in your rec.crg.pdb file after blastermaster runs.

	If you have missing residues, Schrodinger can be used to build them:		If you have missing residues, Schrodinger can be used to build them:

Rstein: /* Useful References */

2019-10-03T17:31:33Z

Useful References

← Older revision		Revision as of 17:31, 3 October 2019
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	<B>SOLVMAP</B>		<B>SOLVMAP</B>

			Shoichet, B. K.; Leach, A. R.; Kuntz, I. D. Ligand solvation in molecular docking. Proteins 1999, 34,4.

	M. M. Mysinger, B. K. Shoichet, Rapid context-dependent ligand desolvation in molecular docking. J. Chem. Inf. Model.50, 1561–1573 (2010). doi:10.1021/ci100214a		M. M. Mysinger, B. K. Shoichet, Rapid context-dependent ligand desolvation in molecular docking. J. Chem. Inf. Model.50, 1561–1573 (2010). doi:10.1021/ci100214a

Rstein: /* Running Blastermaster */

2019-10-03T17:28:31Z

Running Blastermaster

← Older revision		Revision as of 17:28, 3 October 2019
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	Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.		Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.
	Are all residues built in your structure? Blastermaster will not give you an error if they are not.		Are all residues built in your structure? Blastermaster will not give you an error if they are not.
	Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are "CYX" after blastermaster runs.		Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are renamed to "CYX" after blastermaster runs.

	If you have missing residues, Schrodinger can be used to build them:		If you have missing residues, Schrodinger can be used to build them:

Rstein: /* Running Blastermaster */

2019-10-03T17:28:18Z

Running Blastermaster

← Older revision		Revision as of 17:28, 3 October 2019
Line 10:		Line 10:
	Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.		Are there any mutations in your structure? Consider mutating these to WT before running blastermaster.
	Are all residues built in your structure? Blastermaster will not give you an error if they are not.		Are all residues built in your structure? Blastermaster will not give you an error if they are not.
			Does your protein have disulfide bonds? Blastermaster should recognize these, but double check that they are "CYX" after blastermaster runs.

	If you have missing residues, Schrodinger can be used to build them:		If you have missing residues, Schrodinger can be used to build them:

Rstein: /* Running Blastermaster */

2019-10-03T17:26:13Z

Running Blastermaster

← Older revision		Revision as of 17:26, 3 October 2019
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	/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/home/tbalius/zzz.scripts/chimera_dockprep.py rec.pdb out_rec"		/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/home/tbalius/zzz.scripts/chimera_dockprep.py rec.pdb out_rec"

	~~Use~~ the output file "out_rec_polarH.pdb"		From Chimera, use the output file "out_rec_polarH.pdb"

	Check that the newly built residues are in the orientation you want. If they are fine, rename the output file to "rec.pdb", and run blastermaster.		Check that the newly built residues are in the orientation you want. If they are fine, rename the output file to "rec.pdb", and run blastermaster.

Rstein: /* Useful References */

2019-10-03T17:24:58Z

Useful References

← Older revision		Revision as of 17:24, 3 October 2019
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	<B>DOCK</B>		<B>DOCK</B>

	Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin,T. E. A geometric approach to macromolecule-ligand interactions.J. Mol. Biol.1982,161, 269-288.		Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin,T. E. A geometric approach to macromolecule-ligand interactions.J. Mol. Biol.1982,161, 269-288.

	<B>DOCK3.7</B>		<B>DOCK3.7</B>

	R. G. Coleman, M. Carchia, T. Sterling, J. J. Irwin, B. K. Shoichet, Ligand pose and orientational sampling in molecular docking. PLOS ONE 8, e75992 (2013)		R. G. Coleman, M. Carchia, T. Sterling, J. J. Irwin, B. K. Shoichet, Ligand pose and orientational sampling in molecular docking. PLOS ONE 8, e75992 (2013)

	<B>CHEMGRID</B>		<B>CHEMGRID</B>

	Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.		Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.

	<B>REDUCE</B>		<B>REDUCE</B>

	J. M. Word, S. C. Lovell, J. S. Richardson, D. C. Richardson, Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747 (1999). doi:10.1006/jmbi.1998.2401		J. M. Word, S. C. Lovell, J. S. Richardson, D. C. Richardson, Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747 (1999). doi:10.1006/jmbi.1998.2401

	<B>SOLVMAP</B>		<B>SOLVMAP</B>

	M. M. Mysinger, B. K. Shoichet, Rapid context-dependent ligand desolvation in molecular docking. J. Chem. Inf. Model.50, 1561–1573 (2010). doi:10.1021/ci100214a		M. M. Mysinger, B. K. Shoichet, Rapid context-dependent ligand desolvation in molecular docking. J. Chem. Inf. Model.50, 1561–1573 (2010). doi:10.1021/ci100214a

	<B>QNIFFT/DelPhi</B>		<B>QNIFFT/DelPhi</B>

	Gilson, M., Sharp, K. A., Honig, B. (1988). "Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment". J. Comp. Chem. 9:327-335		Gilson, M., Sharp, K. A., Honig, B. (1988). "Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment". J. Comp. Chem. 9:327-335

Rstein at 17:24, 3 October 2019

2019-10-03T17:24:38Z

← Older revision		Revision as of 17:24, 3 October 2019
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	Lastly, the INDOCK file is written		Lastly, the INDOCK file is written


			== Useful References ==

			<B>DOCK</B>
			Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin,T. E. A geometric approach to macromolecule-ligand interactions.J. Mol. Biol.1982,161, 269-288.

			<B>DOCK3.7</B>
			R. G. Coleman, M. Carchia, T. Sterling, J. J. Irwin, B. K. Shoichet, Ligand pose and orientational sampling in molecular docking. PLOS ONE 8, e75992 (2013)

			<B>CHEMGRID</B>
			Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.

			<B>REDUCE</B>
			J. M. Word, S. C. Lovell, J. S. Richardson, D. C. Richardson, Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747 (1999). doi:10.1006/jmbi.1998.2401

			<B>SOLVMAP</B>
			M. M. Mysinger, B. K. Shoichet, Rapid context-dependent ligand desolvation in molecular docking. J. Chem. Inf. Model.50, 1561–1573 (2010). doi:10.1021/ci100214a

			<B>QNIFFT/DelPhi</B>
			Gilson, M., Sharp, K. A., Honig, B. (1988). "Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment". J. Comp. Chem. 9:327-335

			Sharp, K., Honig, B. (1990). "Electrostatic Interactions in Macromolecules: Theory and Applications". Ann. Rev. Biophys. Biophys. Chem 19:301-332.

			Sitkoff et al, J. Phys. Chem, 1994.v 98, 1978-88 "Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models"

			Sharp, K. A. (1995). "Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model". Biopolymers 36:227-243.

Rstein: /* Running Blastermaster */

2019-10-03T17:09:25Z

Running Blastermaster

← Older revision		Revision as of 17:09, 3 October 2019
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	/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/home/tbalius/zzz.scripts/chimera_dockprep.py rec.pdb out_rec"		/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/home/tbalius/zzz.scripts/chimera_dockprep.py rec.pdb out_rec"

	Use the output file "out_rec_polarH.pdb"		Use the output file "out_rec_polarH.pdb"

Rstein: /* Running Blastermaster */

2019-10-03T17:08:00Z

Running Blastermaster

← Older revision		Revision as of 17:08, 3 October 2019
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	$SCHRODINGER/utilities/prepwizard -fillsidechains -noprotassign -noepik -noimpref rec.pdb outrec.pdb		$SCHRODINGER/utilities/prepwizard -fillsidechains -noprotassign -noepik -noimpref rec.pdb outrec.pdb

	Check that the newly built residues are in the orientation you want. ~~Then~~ rename ~~outrec.pdb~~ to rec.pdb.		Alternatively, Chimera can be used to build them:

			/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/home/tbalius/zzz.scripts/chimera_dockprep.py rec.pdb out_rec"

			Use the output file "out_rec_polarH.pdb"

			Check that the newly built residues are in the orientation you want. If they are fine, rename the output file to "rec.pdb", and run blastermaster.

	Then in that directory, run the command:		Then in that directory, run the command: