Chembl2pdb - Revision history

Frodo at 14:46, 21 March 2014

2014-03-21T14:46:36Z

← Older revision		Revision as of 14:46, 21 March 2014
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	[[Category:Tutorials]]		[[Category:Tutorials]]
			[[Category:ChEMBL]]

Therese: 15 revisions

2012-10-08T18:10:29Z

15 revisions

← Older revision	Revision as of 18:10, 8 October 2012
(No difference)

Mysinger: /* GENERATION PROCEDURE */

2011-03-18T21:43:09Z

GENERATION PROCEDURE

← Older revision		Revision as of 21:43, 18 March 2011
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	*Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)		*Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)
	*Step II.: Make a new directory, run the script, and wait a day or two for it to finish		*Step II.: Make a new directory, run the script pointing to the new sql database name, and wait a day or two for it to finish
	mkdir chembl10		mkdir chembl10
	cd chembl10		cd chembl10

Mysinger: /* GENERATION PROCEDURE */

2011-03-18T21:42:29Z

GENERATION PROCEDURE

← Older revision		Revision as of 21:42, 18 March 2011
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	*Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)		*Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)
	*Step II.: Make a new directory, run the script, and wait a day or two for it to finish		*Step II.: Make a new directory, run the script, and wait a day or two for it to finish
	~~```~~mkdir chembl10~~```~~		mkdir chembl10
	~~```~~cd chembl10~~```~~		cd chembl10
	~~```~~/raid3/people/mysinger/pxc/pdb_to_chembl/generate_chembl_map.csh chembl10~~```~~		/raid3/people/mysinger/pxc/pdb_to_chembl/generate_chembl_map.csh chembl10

	[[Category:Tutorials]]		[[Category:Tutorials]]

Mysinger: /* GENERATION PROCEDURE */

2011-03-18T21:41:50Z

GENERATION PROCEDURE

← Older revision		Revision as of 21:41, 18 March 2011
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	In future, if you want to generate the data again, you need to do the following:		In future, if you want to generate the data again, you need to do the following:

	Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)		*Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)
	Step II.: Make a new directory, run the script, and wait a day or two for it to finish		*Step II.: Make a new directory, run the script, and wait a day or two for it to finish
	```mkdir chembl10```		```mkdir chembl10```
	```cd chembl10```		```cd chembl10```

Mysinger: /* GENERATION PROCEDURE */

2011-03-18T21:41:30Z

GENERATION PROCEDURE

← Older revision		Revision as of 21:41, 18 March 2011
Line 35:		Line 35:
	In future, if you want to generate the data again, you need to do the following:		In future, if you want to generate the data again, you need to do the following:

	Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)		Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)
	Step II.: Make a new directory, run the script, and wait a day or two for it to finish		Step II.: Make a new directory, run the script, and wait a day or two for it to finish
	```mkdir chembl10```		```mkdir chembl10```
	```cd chembl10```		```cd chembl10```

Mysinger: New simplified generation procedure

2011-03-18T21:41:04Z

New simplified generation procedure

New page

== CURRENT DATA ==

__ Updated 02/24/2011 __

The current data relating the ChEMBL09 protein targets to structures on the PDB can be found at:

'''/raid3/people/mysinger/pxc/pdb_to_chembl/chembl09'''

There are 3 subfolders:

- '''uniprot''': categorized by target uniprot id

- '''pdb_ligand''': all pdb codes that have a bound ligand (as defined by be_blasti.csh script from DOCKBlaster)
with the corresponding activity data from ChEMBL (actives.smi)

- '''pdb_other''': all pdb codes that do NOT have a bound crystal ligand (as defined by be_blasti.csh script from DOCKBlaster)
with the corresponding actives from chEMBL(actives.smi)

In order to get some statistics: how many pdb codes, how many targets have ChEMBL ligands, you can simply count the number of subfolders in each "byXXX" folder.

eg: How many UniProt targets have ChEMBL ligands?
% cd uniprot
% wc -l uniprot

eg: How many pdb structures have ChEMBL actives and a bound crystal ligand?
% cd bypdb_ligand/
% ls -d ????| wc -l

eg: How many pdb structures have ChEMBL actives BUT WITHOUT a bound crystal ligand?
% cd pdb_other/
% ls -d ???? | wc -l

== GENERATION PROCEDURE ==

In future, if you want to generate the data again, you need to do the following:

Step I: Load new ChEMBL SQL database into zincdb1 ( do this only if there is a new ChEMBL release)
Step II.: Make a new directory, run the script, and wait a day or two for it to finish
```mkdir chembl10```
```cd chembl10```
```/raid3/people/mysinger/pxc/pdb_to_chembl/generate_chembl_map.csh chembl10```

[[Category:Tutorials]]