DOCK 3.7 tutorial based on Webinar 2017/06/28 - Revision history

TBalius: /* Scenario 2: */

2017-10-03T15:31:22Z

Scenario 2:

← Older revision		Revision as of 15:31, 3 October 2017
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	csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi		csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi

	For more information see the page: [[Ligand_preparation_-_20170424]]		For more information see the page: [[Ligand_preparation_-_20170424]]

2017-10-03T15:29:54Z

Scenario 2:

← Older revision		Revision as of 15:29, 3 October 2017
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	${DOCKBASE}/ligand/generate/build_database_ligand.sh -H 7.4 ligands_12_from_chembl.smi		${DOCKBASE}/ligand/generate/build_database_ligand.sh -H 7.4 ligands_12_from_chembl.smi

	csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi		csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi

	For more information see the page: [[Ligand_preparation_-_20170424]]		For more information see the page: [[Ligand_preparation_-_20170424]]

2017-10-03T15:29:03Z

Scenario 2:

← Older revision		Revision as of 15:29, 3 October 2017
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	grep -v ligand dude-decoys/decoys/decoys.P*.picked \| awk -F: '{print $2}' \| awk '{print $1 " " $2}' > ! decoys.smi		grep -v ligand dude-decoys/decoys/decoys.P*.picked \| awk -F: '{print $2}' \| awk '{print $1 " " $2}' > ! decoys.smi

	${DOCKBASE}/ligand/generate/build_database_ligand.sh -H 7.4 ligands_12_from_chembl.smi		${DOCKBASE}/ligand/generate/build_database_ligand.sh -H 7.4 ligands_12_from_chembl.smi

	csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi		csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi

	For more information see the page: [[Ligand_preparation_-_20170424]]		For more information see the page: [[Ligand_preparation_-_20170424]]

2017-10-03T15:28:31Z

Scenario 2:

← Older revision		Revision as of 15:28, 3 October 2017
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	csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi		csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi
	[[Ligand_preparation_-_20170424]]
			For more information see the page: [[Ligand_preparation_-_20170424]]

2017-10-03T15:25:19Z

Scenario 2:

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	Process the XLS file into the a smiles file called "ligands_12_from_chembl.smi" with the smiles in the first column and the name in the second column.		Process the XLS file into the a smiles file called "ligands_12_from_chembl.smi" with the smiles in the first column and the name in the second column.

			cat bioactivity-17_20_35_00.xls \| grep -v "CMPD_CHEMBLID" \| head -12 \| awk '{print $10 " " $1}' > ligands_12_from_chembl.smi

	Generate Decoy Smiles File		Generate Decoy Smiles File

2017-10-03T15:20:58Z

Scenario 2:

← Older revision		Revision as of 15:20, 3 October 2017
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	[[File:DOCK3.7tuturial.2017.06.28.7.png\|thumb\|center\|500px\|Obtain smiles from Chembl.]]		[[File:DOCK3.7tuturial.2017.06.28.7.png\|thumb\|center\|500px\|Obtain smiles from Chembl.]]

			Process the XLS file into the a smiles file called "ligands_12_from_chembl.smi" with the smiles in the first column and the name in the second column.


	Generate Decoy Smiles File		Generate Decoy Smiles File

2017-06-30T16:05:03Z

← Older revision		Revision as of 16:05, 30 June 2017
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	This tuturial expands on a webinar presentation to the SBGrid [https://sbgrid.org/news/sbgrid-lunch-break-trent-balius]		This tuturial expands on a webinar presentation to the SBGrid [https://sbgrid.org/news/sbgrid-lunch-break-trent-balius]

			Find the Youtube video here: [https://www.youtube.com/watch?v=FAjGbZPH8ko video]

	= Scenario 1: =		= Scenario 1: =

2017-06-29T18:32:58Z

Scenario 2:

← Older revision		Revision as of 18:32, 29 June 2017
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	Submit docking jobs:		Submit docking jobs:
	$DOCKBASE/docking/submit/submit.csh		$DOCKBASE/docking/submit/submit.csh

			Process results combining results and get the best poses:

			$DOCKBASE/analysis/extract_all.py
			$DOCKBASE/analysis/getposes.py

			Calculate enrichments:

			$DOCKBASE/analysis/enrich.py -i . -l databases/ligands_names.txt -d databases/decoys_names.txt
			$DOCKBASE/analysis/plots.py -i . -l databases/ligands_names.txt -d databases/decoys_names.txt

			[[File:DOCK3.7tuturial.2017.06.28.9.png\|thumb\|center\|500px\|Enrichment quanified using log-adjusted AUC curves.]]

2017-06-29T18:27:01Z

Scenario 2:

← Older revision		Revision as of 18:27, 29 June 2017
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	[[File:DOCK3.7tuturial.2017.06.28.8.png\|thumb\|center\|500px\|Generate property matched decoys from DUD-E webserver.]]		[[File:DOCK3.7tuturial.2017.06.28.8.png\|thumb\|center\|500px\|Generate property matched decoys from DUD-E webserver.]]


			If the system is in DUD-E, You may download ready to dock databases here:
			http://autodude.docking.org/

			Here I just used the first 12 ligands from Chembl

			Generated decoys using DUD-E webserver
			Use the link in email:

			wget http://dude.docking.org/generate/results/4094969748/dude-decoys.tar.gz
			tar -xzvf dude-decoys.tar.gz

			grep -v ligand dude-decoys/decoys/decoys.P*.picked \| awk -F: '{print $2}' \| awk '{print $1 " " $2}' > ! decoys.smi

			${DOCKBASE}/ligand/generate/build_database_ligand.sh -H 7.4 ligands_12_from_chembl.smi

			csh wraper_queue_build_smiles_ligand_mod_corina.csh decoys.smi
			[[Ligand_preparation_-_20170424]]


			Make a list of all the databases:

			ls /path/databases/ligands_12_from_chembl/CHEMBL/.db2.gz /path/databases/decoys/sgejob_/finished/C/*.db2.gz > ! ligands_decoys.sdi

			awk '{print $2}' databases/ligands_12_from_chembl.smi > databases/ligands_names.txt
			awk '{print $2}' databases/decoys.smi > databases/decoys_names.txt

			Make directories for docking:

			$DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py ./ ligands_decoys databases/ligands_decoys.sdi 100 count

			Submit docking jobs:
			$DOCKBASE/docking/submit/submit.csh

2017-06-29T18:24:25Z

Scenario 2:

← Older revision		Revision as of 18:24, 29 June 2017
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	Use docking to test enrichment capabilities of Epidermal Growth Factor Receptor using 12 ligands and DUD-E property matched decoys		Use docking to test enrichment capabilities of Epidermal Growth Factor Receptor using 12 ligands and DUD-E property matched decoys

			Get Known Ligands for Docking
			https://www.ebi.ac.uk/chembl/target/inspect/CHEMBL203


	[[File:DOCK3.7tuturial.2017.06.28.6.png\|thumb\|center\|500px\|Find your target on Chembl.]]		[[File:DOCK3.7tuturial.2017.06.28.6.png\|thumb\|center\|500px\|Find your target on Chembl.]]

			Get Known Ligands for Docking

	[[File:DOCK3.7tuturial.2017.06.28.7.png\|thumb\|center\|500px\|Obtain smiles from Chembl.]]		[[File:DOCK3.7tuturial.2017.06.28.7.png\|thumb\|center\|500px\|Obtain smiles from Chembl.]]

			Generate Decoy Smiles File
			http://dude.docking.org/generate


	[[File:DOCK3.7tuturial.2017.06.28.8.png\|thumb\|center\|500px\|Generate property matched decoys from DUD-E webserver.]]		[[File:DOCK3.7tuturial.2017.06.28.8.png\|thumb\|center\|500px\|Generate property matched decoys from DUD-E webserver.]]