Talk:Syn/anti lateral protonation - Revision history

Wim Nerinckx at 10:49, 17 November 2009

2009-11-17T10:49:13Z

Spencer Williams: /* Order of columns */

2009-11-17T04:13:33Z

Order of columns

Spencer Williams: /* Order of columns */

2009-11-17T04:12:58Z

Order of columns

Wim Nerinckx at 10:31, 16 November 2009

2009-11-16T10:31:14Z

Wim Nerinckx at 10:30, 16 November 2009

2009-11-16T10:30:10Z

Harry Brumer: /* Link to PDB data */ new section

2009-11-16T08:28:23Z

Link to PDB data: new section

Harry Brumer: /* Order of columns */

2009-11-13T15:05:54Z

Order of columns

Wim Nerinckx at 10:08, 13 November 2009

2009-11-13T10:08:14Z

Harry Brumer: /* Order of columns */ new section

2009-11-13T08:37:49Z

Order of columns: new section

Wim Nerinckx at 23:21, 12 November 2009

2009-11-12T23:21:18Z

@@ Line 72: / Line 72: @@
 * I agree regarding the choice of PDB file.  I have an idea for easy linking to the PDB that I will try out.  [[User:Harry Brumer|Harry Brumer]] 15:05, 13 November 2009 (UTC)
 * I think that the structures of imidazole/tetrazole/lactam oxime-containing enzymes are of special interest as these inhibitors were designed specifically to probe for anti protonation. Could they be added, along with an annotation?[[User:Spencer Williams|Spencer Williams]] 04:12, 17 November 2009 (UTC)
 == Link to PDB data ==

@@ Line 71: / Line 71: @@
 * I agree regarding the choice of PDB file.  I have an idea for easy linking to the PDB that I will try out.  [[User:Harry Brumer|Harry Brumer]] 15:05, 13 November 2009 (UTC)
-* I think that the structures of imidazole/tetrazole-containing enzymes are of special interest as these inhibitors were designed specifically to probe for anti protonation. Could they be added, along with an annotation?[[User:Spencer Williams|Spencer Williams]] 04:12, 17 November 2009 (UTC)
+* I think that the structures of imidazole/tetrazole/lactam oxime-containing enzymes are of special interest as these inhibitors were designed specifically to probe for anti protonation. Could they be added, along with an annotation?[[User:Spencer Williams|Spencer Williams]] 04:12, 17 November 2009 (UTC)
 == Link to PDB data ==

← Older revision		Revision as of 04:12, 17 November 2009
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	* I agree regarding the choice of PDB file. I have an idea for easy linking to the PDB that I will try out. [[User:Harry Brumer\|Harry Brumer]] 15:05, 13 November 2009 (UTC)		* I agree regarding the choice of PDB file. I have an idea for easy linking to the PDB that I will try out. [[User:Harry Brumer\|Harry Brumer]] 15:05, 13 November 2009 (UTC)
		+	* I think that the structures of imidazole/tetrazole-containing enzymes are of special interest as these inhibitors were designed specifically to probe for anti protonation. Could they be added, along with an annotation?[[User:Spencer Williams\|Spencer Williams]] 04:12, 17 November 2009 (UTC)

	== Link to PDB data ==		== Link to PDB data ==

← Older revision		Revision as of 10:31, 16 November 2009
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	[[User:Harry Brumer\|Harry Brumer]] 08:28, 16 November 2009 (UTC)		[[User:Harry Brumer\|Harry Brumer]] 08:28, 16 November 2009 (UTC)
−	* ~~Protopedia~~ now linked throughout in the pdb-column. Very nice! [[User:Wim Nerinckx\|Wim Nerinckx]] 10:30, 16 November 2009 (UTC)	+	* Proteopedia now linked throughout in the pdb-column. Very nice! [[User:Wim Nerinckx\|Wim Nerinckx]] 10:30, 16 November 2009 (UTC)

← Older revision		Revision as of 10:30, 16 November 2009
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	[[User:Harry Brumer\|Harry Brumer]] 08:28, 16 November 2009 (UTC)		[[User:Harry Brumer\|Harry Brumer]] 08:28, 16 November 2009 (UTC)
		+	* Protopedia now linked throughout in the pdb-column. Very nice! [[User:Wim Nerinckx\|Wim Nerinckx]] 10:30, 16 November 2009 (UTC)

← Older revision		Revision as of 08:28, 16 November 2009
Line 71:		Line 71:

	* I agree regarding the choice of PDB file. I have an idea for easy linking to the PDB that I will try out. [[User:Harry Brumer\|Harry Brumer]] 15:05, 13 November 2009 (UTC)		* I agree regarding the choice of PDB file. I have an idea for easy linking to the PDB that I will try out. [[User:Harry Brumer\|Harry Brumer]] 15:05, 13 November 2009 (UTC)
		+
		+	== Link to PDB data ==
		+
		+	I've implemented a fairly simple link to PDB data using the template page [[:Template:PDBlink]]. At the moment, this points to [http://www.proteopedia.org/ Proteopedia], which I think has a bit nicer look than the RCSB PDB entry pages (and besides, [http://www.proteopedia.org/ Proteopedia] is a wiki!).
		+
		+	[[User:Harry Brumer\|Harry Brumer]] 08:28, 16 November 2009 (UTC)

← Older revision		Revision as of 15:05, 13 November 2009
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	I however - with respect - disagree on the "family first" (often an empty enzyme) as pdb-example here. I think that the pdb-example here should be one in which the syn or anti position is clear to see. So my order of preference would be 1) Michaelis-type spanning the crucial subsites -1/+1, 2) glycosyl-enzyme intermediate, 3) product if both plus +1 and -1 are occupied, 4) product if several of the minus subsites are occupied including -1. The interested visitor could then easily download the pdb-example (can the pdb-entry in the table be made "clickable" towards the RCSB as in CAZy?), zoom towards the ligand and indicated residues, and see syn or anti for himself. [[User:Wim Nerinckx\|Wim Nerinckx]] 10:08, 13 November 2009 (UTC)		I however - with respect - disagree on the "family first" (often an empty enzyme) as pdb-example here. I think that the pdb-example here should be one in which the syn or anti position is clear to see. So my order of preference would be 1) Michaelis-type spanning the crucial subsites -1/+1, 2) glycosyl-enzyme intermediate, 3) product if both plus +1 and -1 are occupied, 4) product if several of the minus subsites are occupied including -1. The interested visitor could then easily download the pdb-example (can the pdb-entry in the table be made "clickable" towards the RCSB as in CAZy?), zoom towards the ligand and indicated residues, and see syn or anti for himself. [[User:Wim Nerinckx\|Wim Nerinckx]] 10:08, 13 November 2009 (UTC)
		+
		+	* I agree regarding the choice of PDB file. I have an idea for easy linking to the PDB that I will try out. [[User:Harry Brumer\|Harry Brumer]] 15:05, 13 November 2009 (UTC)

← Older revision		Revision as of 10:08, 13 November 2009
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	[[User:Harry Brumer\|Harry Brumer]] 08:37, 13 November 2009 (UTC)		[[User:Harry Brumer\|Harry Brumer]] 08:37, 13 November 2009 (UTC)
		+	* Your proposed column order is great! Will do that.
		+
		+	I however - with respect - disagree on the "family first" (often an empty enzyme) as pdb-example here. I think that the pdb-example here should be one in which the syn or anti position is clear to see. So my order of preference would be 1) Michaelis-type spanning the crucial subsites -1/+1, 2) glycosyl-enzyme intermediate, 3) product if both plus +1 and -1 are occupied, 4) product if several of the minus subsites are occupied including -1. The interested visitor could then easily download the pdb-example (can the pdb-entry in the table be made "clickable" towards the RCSB as in CAZy?), zoom towards the ligand and indicated residues, and see syn or anti for himself. [[User:Wim Nerinckx\|Wim Nerinckx]] 10:08, 13 November 2009 (UTC)

← Older revision		Revision as of 08:37, 13 November 2009
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	* The question from Spencer is pertinent and now gave me this thought: wouldn't it be better to move the pdb column (instead of at the near-end where it is now) to right before the column with "General acid", and also rename it as "Example PDB ID"? Then it should be at once clear that the residue numbering is for the structure in the example pdb. [[User:Wim Nerinckx\|Wim Nerinckx]] 18:55, 12 November 2009 (UTC)		* The question from Spencer is pertinent and now gave me this thought: wouldn't it be better to move the pdb column (instead of at the near-end where it is now) to right before the column with "General acid", and also rename it as "Example PDB ID"? Then it should be at once clear that the residue numbering is for the structure in the example pdb. [[User:Wim Nerinckx\|Wim Nerinckx]] 18:55, 12 November 2009 (UTC)
	* Update: tried it first on a preview and found it much better, so I already did it.[[User:Wim Nerinckx\|Wim Nerinckx]] 23:21, 12 November 2009 (UTC)		* Update: tried it first on a preview and found it much better, so I already did it.[[User:Wim Nerinckx\|Wim Nerinckx]] 23:21, 12 November 2009 (UTC)
		+
		+	== Order of columns ==
		+
		+	It occurred to me that it might be a bit more logical to re-order the columns as follows:
		+
		+	'''family, clan, fold, anom. specificity, mechanism, ''syn/anti'', example PDB, enzyme, organism, ligand, general acid, nucleophile/G.B., reference'''
		+
		+	This groups all the key ''general'' mechanistic/structural details in the first 6 columns. Then, the reader is directed to one ''specific'' example structure, via the PDB ID, whose details are given. For example, the specific position of the general acid and nucleophile are largely irrelevant, except to someone who actually opens the structure and looks in detail.
		+
		+	I would also suggest the following guideline: The PDB file and reference should be chose to correspond with the first determined structure in the family (listed in the "Family Firsts" section), ''unless'' there is different reference in which the syn/anti concept is specifically discussed.
		+
		+	[[User:Harry Brumer\|Harry Brumer]] 08:37, 13 November 2009 (UTC)

← Older revision		Revision as of 23:21, 12 November 2009
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	== Suggestion to move the pdb column ==		== Suggestion to move the pdb column ==

−	The question from Spencer is pertinent and now gave me this thought: wouldn't it be better to move the pdb column (instead of at the near-end where it is now) to right before the column with "General acid", and also rename it as "Example PDB ID"? Then it should be at once clear that the residue numbering is for the structure in the example pdb. [[User:Wim Nerinckx\|Wim Nerinckx]] 18:55, 12 November 2009 (UTC)	+	* The question from Spencer is pertinent and now gave me this thought: wouldn't it be better to move the pdb column (instead of at the near-end where it is now) to right before the column with "General acid", and also rename it as "Example PDB ID"? Then it should be at once clear that the residue numbering is for the structure in the example pdb. [[User:Wim Nerinckx\|Wim Nerinckx]] 18:55, 12 November 2009 (UTC)
		+	* Update: tried it first on a preview and found it much better, so I already did it.[[User:Wim Nerinckx\|Wim Nerinckx]] 23:21, 12 November 2009 (UTC)