Structure based ligand discovery - Revision history

Therese: 8 revisions

2012-10-08T20:32:25Z

8 revisions

← Older revision	Revision as of 20:32, 8 October 2012
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Frodo at 21:23, 12 February 2009

2009-02-12T21:23:55Z

← Older revision		Revision as of 21:23, 12 February 2009
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	Structure based ligand discovery is the use of		Structure based ligand discovery is the use of
	a macromolecular (usually protein) structure to discover new ligands - small molecules that		a macromolecular (usually protein) structure to discover new ligands - small molecules that
	bind to the protein. There are at least three ways to do this:		bind stoichiometrically to the protein. There are at least three ways to do this:

	* 1. Have an expert look at the model, and draw a molecule that complements the binding site.		* 1. Have an expert look at the model, and draw a molecule that complements the binding site.

Frodo at 02:08, 12 February 2009

2009-02-12T02:08:25Z

← Older revision		Revision as of 02:08, 12 February 2009
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	The problem with method #1 is that it is very labor intensive, and that any compound proposed may be difficult and/or expensive to acquire. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitation. It can also be, relatively speaking, slow.		The problem with method #1 is that it is very labor intensive, and that any compound proposed may be difficult and/or expensive to acquire. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitation. It can also be, relatively speaking, slow.

	The third approach, docking, is the one taken by [[DOCK]] and its graphical user interface, [[DOCK Blaster]].		The third approach, docking, is the one taken by [[DOCK]] and its graphical user interface, [[DOCK Blaster]]. It is particularly pragmatic when used to screen a database of compounds that can be acquired rapidly, such as those in [[ZINC]], because the time from hypothesis to experimental test can be very short, and the project can progress rapidly.

	[[Category:DOCK]]		[[Category:DOCK]]

Frodo at 02:07, 12 February 2009

2009-02-12T02:07:05Z

← Older revision		Revision as of 02:07, 12 February 2009
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	bind to the protein. There are at least three ways to do this:		bind to the protein. There are at least three ways to do this:

	* 1. ~~have~~ an expert look at the model, and draw a molecule that complements the binding site.		* 1. Have an expert look at the model, and draw a molecule that complements the binding site.
	* 2. Perform #1 using an automatic program. This is called [[de novo design]].		* 2. Perform #1 using an automatic program. This is called [[de novo design]].
	* 3. Dock a database of small molecules into the binding site, and rank them from best to worst.		* 3. Dock a database of small molecules into the binding site, and rank them from best to worst.

Frodo at 02:06, 12 February 2009

2009-02-12T02:06:54Z

← Older revision		Revision as of 02:06, 12 February 2009
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	Structure based ligand discovery is the use of		Structure based ligand discovery is the use of
	a macromolecular (usually protein) structure to discover new ligands. ~~At a high level, there~~ are three ways to ~~go about~~ this:		a macromolecular (usually protein) structure to discover new ligands - small molecules that
			bind to the protein. There are at least three ways to do this:

	* 1. have an expert look at the model, and draw a molecule that complements the binding site.		* 1. have an expert look at the model, and draw a molecule that complements the binding site.

Frodo at 01:16, 12 February 2009

2009-02-12T01:16:58Z

← Older revision		Revision as of 01:16, 12 February 2009
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	* 3. Dock a database of small molecules into the binding site, and rank them from best to worst.		* 3. Dock a database of small molecules into the binding site, and rank them from best to worst.

	The problem with method #1 is that it is very labor intensive, and that any compound ~~invented~~ may be difficult and/or expensive to ~~make~~. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this ~~limitations~~. It can also be, relatively speaking, slow.		The problem with method #1 is that it is very labor intensive, and that any compound proposed may be difficult and/or expensive to acquire. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitation. It can also be, relatively speaking, slow.

	The third approach, docking, is the one taken by [[DOCK]] and its graphical user interface, [[DOCK Blaster]].		The third approach, docking, is the one taken by [[DOCK]] and its graphical user interface, [[DOCK Blaster]].

	[[Category:DOCK]]		[[Category:DOCK]]

Frodo at 01:16, 12 February 2009

2009-02-12T01:16:15Z

← Older revision		Revision as of 01:16, 12 February 2009
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	a macromolecular (usually protein) structure to discover new ligands. At a high level, there are three ways to go about this:		a macromolecular (usually protein) structure to discover new ligands. At a high level, there are three ways to go about this:

	1. have an expert look at the model, and draw a molecule that complements the binding site.		* 1. have an expert look at the model, and draw a molecule that complements the binding site.
	2. Perform #1 using an automatic program. This is called [[de novo design]].		* 2. Perform #1 using an automatic program. This is called [[de novo design]].
	3. Dock a database of small molecules into the binding site, and rank them from best to worst.		* 3. Dock a database of small molecules into the binding site, and rank them from best to worst.

	The problem with method #1 is that it is very labor intensive, and that any compound invented may be difficult and/or expensive to make. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitations. It can also be, relatively speaking, slow.		The problem with method #1 is that it is very labor intensive, and that any compound invented may be difficult and/or expensive to make. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitations. It can also be, relatively speaking, slow.

Frodo at 01:15, 12 February 2009

2009-02-12T01:15:50Z

← Older revision		Revision as of 01:15, 12 February 2009
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	Structure based ligand discovery is the use of		Structure based ligand discovery is the use of
	a macromolecular (usually protein) structure to discover new ~~liggands~~. At a high level, there are three ways to go about this:		a macromolecular (usually protein) structure to discover new ligands. At a high level, there are three ways to go about this:

	1. have an expert look at the model, and draw a molecule that complements the binding site.		1. have an expert look at the model, and draw a molecule that complements the binding site.
	2. Perform #1 using an automatic program. This is called [[~~denovo~~ design]].		2. Perform #1 using an automatic program. This is called [[de novo design]].
	3. Dock a database of small molecules into the binding site, and rank them from best to worst.		3. Dock a database of small molecules into the binding site, and rank them from best to worst.

Frodo at 00:54, 12 February 2009

2009-02-12T00:54:51Z

New page

Structure based ligand discovery is the use of
a macromolecular (usually protein) structure to discover new liggands. At a high level, there are three ways to go about this:

1. have an expert look at the model, and draw a molecule that complements the binding site.
2. Perform #1 using an automatic program. This is called [[denovo design]].
3. Dock a database of small molecules into the binding site, and rank them from best to worst.

The problem with method #1 is that it is very labor intensive, and that any compound invented may be difficult and/or expensive to make. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitations. It can also be, relatively speaking, slow.

The third approach, docking, is the one taken by [[DOCK]] and its graphical user interface, [[DOCK Blaster]].

[[Category:DOCK]]