3qot - Revision history

OCA: Redirecting to 5i18

OCA — Fri, 26 Feb 2016 17:56:01 GMT

Redirecting to 5i18

←Older revision		Revision as of 17:56, 26 February 2016
Line 1:		Line 1:
-	~~==Crystal Structure of Human Germline Antibody 1-69/B3==~~	+	#REDIRECT [[5i18]] This PDB entry is obsolete and replaced by 5i18
-	~~<StructureSection load='3qot' size='340' side='right' caption='~~[[~~3qot]], [[Resolution\|resolution]] 1.90Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[3qot~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QOT FirstGlance]. <br>	+
-	~~</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>~~	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qot RCSB], [http://www.ebi.ac.uk/pdbsum/3qot PDBsum]</span></td></tr>	+
-	~~</table>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	A blinded study to assess the state of the art in three-dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high-resolution x-ray Fab crystal structures covering a wide range of antigen-binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x-ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 A. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 A. H3 prediction yielded rmsd values around 3.0 A for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011; (c) 2011 Wiley-Liss, Inc.	+
-		+
-	Antibody modeling assessment.,Almagro JC, Beavers MP, Hernandez-Guzman F, Maier J, Shaulsky J, Butenhof K, Labute P, Thorsteinson N, Kelly K, Teplyakov A, Luo J, Sweet R, Gilliland GL Proteins. 2011 Nov;79(11):3050-66. doi: 10.1002/prot.23130. Epub 2011 Sep, 21. PMID:21935986<ref>PMID:21935986</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Homo sapiens]]~~	+
-	~~[[Category: Gilliland, G]]~~	+
-	~~[[Category: Malia, T]]~~	+
-	~~[[Category: Obmolova, G]]~~	+
-	~~[[Category: Teplyakov, A]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin fold]]~~	+
-	~~[[Category: Monoclonal antibody]]~~	+

OCA at 21:54, 3 January 2015

OCA — Sat, 03 Jan 2015 21:54:50 GMT

←Older revision		Revision as of 21:54, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QOT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QOT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qot RCSB], [http://www.ebi.ac.uk/pdbsum/3qot PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qot RCSB], [http://www.ebi.ac.uk/pdbsum/3qot PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 12:		Line 12:
	Antibody modeling assessment.,Almagro JC, Beavers MP, Hernandez-Guzman F, Maier J, Shaulsky J, Butenhof K, Labute P, Thorsteinson N, Kelly K, Teplyakov A, Luo J, Sweet R, Gilliland GL Proteins. 2011 Nov;79(11):3050-66. doi: 10.1002/prot.23130. Epub 2011 Sep, 21. PMID:21935986<ref>PMID:21935986</ref>		Antibody modeling assessment.,Almagro JC, Beavers MP, Hernandez-Guzman F, Maier J, Shaulsky J, Butenhof K, Labute P, Thorsteinson N, Kelly K, Teplyakov A, Luo J, Sweet R, Gilliland GL Proteins. 2011 Nov;79(11):3050-66. doi: 10.1002/prot.23130. Epub 2011 Sep, 21. PMID:21935986<ref>PMID:21935986</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 19:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Gilliland, G.]]	+	[[Category: Gilliland, G]]
-	[[Category: Malia, T.]]	+	[[Category: Malia, T]]
-	[[Category: Obmolova, G.]]	+	[[Category: Obmolova, G]]
-	[[Category: Teplyakov, A.]]	+	[[Category: Teplyakov, A]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Immunoglobulin fold]]		[[Category: Immunoglobulin fold]]
	[[Category: Monoclonal antibody]]		[[Category: Monoclonal antibody]]

OCA at 05:26, 4 June 2014

OCA — Wed, 04 Jun 2014 05:26:48 GMT

←Older revision		Revision as of 05:26, 4 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3qot.~~png~~\|~~left\|200px~~]]	+	==Crystal Structure of Human Germline Antibody 1-69/B3==
		+	<StructureSection load='3qot' size='340' side='right' caption='[[3qot]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QOT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qot RCSB], [http://www.ebi.ac.uk/pdbsum/3qot PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A blinded study to assess the state of the art in three-dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high-resolution x-ray Fab crystal structures covering a wide range of antigen-binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x-ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 A. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 A. H3 prediction yielded rmsd values around 3.0 A for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011; (c) 2011 Wiley-Liss, Inc.

-	<!--	+	Antibody modeling assessment.,Almagro JC, Beavers MP, Hernandez-Guzman F, Maier J, Shaulsky J, Butenhof K, Labute P, Thorsteinson N, Kelly K, Teplyakov A, Luo J, Sweet R, Gilliland GL Proteins. 2011 Nov;79(11):3050-66. doi: 10.1002/prot.23130. Epub 2011 Sep, 21. PMID:21935986<ref>PMID:21935986</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3qot"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3qot\| PDB=3qot \| SCENE= }}~~	+

-	~~===Crystal Structure of Human Germline Antibody 1-69~~/~~B3===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21935986}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21935986 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21935986}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3qot]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021935986<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Gilliland, G.]]		[[Category: Gilliland, G.]]

OCA at 07:38, 30 October 2011

OCA — Sun, 30 Oct 2011 07:38:02 GMT

←Older revision		Revision as of 07:38, 30 October 2011
Line 1:		Line 1:
-	[[Image:3qot.~~jpg~~\|left\|200px]]	+	[[Image:3qot.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal Structure of Human Germline Antibody 1-69/B3===		===Crystal Structure of Human Germline Antibody 1-69/B3===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21935986}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21935986 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21935986}}

	==About this Structure==		==About this Structure==
	[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA].		[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021935986</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Gilliland, G.]]		[[Category: Gilliland, G.]]

OCA at 06:15, 10 August 2011

OCA — Wed, 10 Aug 2011 06:15:43 GMT

←Older revision		Revision as of 06:15, 10 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qot.jpg\|left\|200px]]

-	The ~~entry 3qot~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qot", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qot\| PDB=3qot \| SCENE= }}

-	~~Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.~~	+	===Crystal Structure of Human Germline Antibody 1-69/B3===

-	~~Description: Crystal~~ Structure ~~of Human Germline Antibody 1~~-69/B3	+
		+	==About this Structure==
		+	[[3qot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOT OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Gilliland, G.]]
		+	[[Category: Malia, T.]]
		+	[[Category: Obmolova, G.]]
		+	[[Category: Teplyakov, A.]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin fold]]
		+	[[Category: Monoclonal antibody]]

OCA at 06:06, 9 March 2011

OCA — Wed, 09 Mar 2011 06:06:04 GMT

←Older revision		Revision as of 06:06, 9 March 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3qot is ON HOLD	+	The entry 3qot is ON HOLD until Paper Publication

	Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.		Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.

	Description: Crystal Structure of Human Germline Antibody 1-69/B3		Description: Crystal Structure of Human Germline Antibody 1-69/B3

OCA at 09:39, 23 February 2011

OCA — Wed, 23 Feb 2011 09:39:35 GMT

←Older revision		Revision as of 09:39, 23 February 2011
Line 5:		Line 5:
	Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.		Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.

-	Description: ~~CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY~~ 1-69/B3	+	Description: Crystal Structure of Human Germline Antibody 1-69/B3

OCA: Protected "3qot" [edit=sysop:move=sysop]

OCA — Wed, 16 Feb 2011 05:23:53 GMT

Protected "3qot" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 16 February 2011

OCA: New page: '''Unreleased structure''' The entry 3qot is ON HOLD Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G. Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY 1-69/B3

OCA — Wed, 16 Feb 2011 05:23:53 GMT

New page: '''Unreleased structure''' The entry 3qot is ON HOLD Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G. Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY 1-69/B3

New page

'''Unreleased structure'''

The entry 3qot is ON HOLD

Authors: Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.

Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY 1-69/B3