Features of your target structure - Revision history

Therese: 4 revisions

2012-10-08T20:24:11Z

4 revisions

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Revision as of 20:24, 8 October 2012

JohnIrwin at 21:19, 20 September 2007

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	== Other situation not listed here ==		== Other situation not listed here ==


			[[Category:DOCK Blaster]]
			[[Category:Preparer]]
			[[Category:Opinion]]

Frodo at 17:41, 21 September 2006

2006-09-21T17:41:06Z

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	== Dimer or multimer ==		== Dimer or multimer ==
			Use PQS.ebi.ac.uk to check multimeric state.
			Is the binding site near a protein-protein interface? If not, use the monomer and ignore the multimeric state. The additional complexities of including a larger structure do not outweigh the more accurate electrostatic potential, in general.
			However, if the binding site is within say 6 A of the protein-protein interface, then at least a fragment of the second protein must be used in the model. From 6-10 A it is a judgement call, but is probably advisable to include
			Watch out also for ligand binding that significantly affects the relative orientation of the two proteins.

	== CYS near binding site ==		== CYS near binding site ==

Frodo: Features of your crystal structure moved to Features of your target structure: may not be a crystal structure at all

2006-09-21T17:23:36Z

Features of your crystal structure moved to Features of your target structure: may not be a crystal structure at all

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Revision as of 17:23, 21 September 2006

Frodo at 17:22, 21 September 2006

2006-09-21T17:22:13Z

New page

Depending on the structural features of the target model, you may need to take special steps to prepare for docking. Many of the following points are relevant no matter which docking program you may use. Comments that are specific to a particular version or particular kind of docking program are noted.

== Covalent inhibitor bound ==
If the target model you wish to dock to has a covalent inhibitor bound, your first step is obviously to remove the inhibitor. You should also keep in mind, however, that the covalently bound ligand may have distorted the active site in ways that a non-covalently bound ligand would not. If you have access to a structure with a non-covalently bound ligand, examine the differences - it may well be preferable to use the non-covalently bound ligand form of the target.

== Non-covalent inhibitor bound ==

== Dimer or multimer ==

== CYS near binding site ==

== Incomplete side chains, missing loops ==

== Active site location unknown or uncertain ==

== ANISO model ==

== Disorder ==

== Flexible side chains in binding site ==

== Very large binding pocket ==

== Very small binding pocket ==

== Cofactor ==

== Metal ==

== Structural water ==

== Open and closed forms of pocket available ==

== Very positively charged site ==

== Very hydrophobic pocket ==

== HIS in active site ==

== Other situation not listed here ==