5nbi - Revision history

OCA at 12:44, 15 November 2023

2023-11-15T12:44:16Z

←Older revision		Revision as of 12:44, 15 November 2023
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	==Principles for computational design of antibodies==		==Principles for computational design of antibodies==
-	<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5nbi' size='340' side='right'caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NBI FirstGlance]. <br>
-	</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [~~http~~://pdbe.org/5nbi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [https://pdbe.org/5nbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [https://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Synthetic construct sequences~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dym, O~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Fleishman, S J~~]]	+	[[Category: Dym O]]
-	[[Category: ~~Antibody]]~~	+	[[Category: Fleishman SJ]]
-	~~[[Category: Immune system~~]]	+

OCA at 07:24, 21 February 2019

2019-02-21T07:24:04Z

←Older revision		Revision as of 07:24, 21 February 2019
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	<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus coli" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBI FirstGlance]. <br>
	</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [http://pdbe.org/5nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [http://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>		</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [http://pdbe.org/5nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [http://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus coli migula 1895~~]]	+	[[Category: Synthetic construct sequences]]
	[[Category: Dym, O]]		[[Category: Dym, O]]
	[[Category: Fleishman, S J]]		[[Category: Fleishman, S J]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 10:18, 8 November 2017

2017-11-08T10:18:46Z

←Older revision		Revision as of 10:18, 8 November 2017
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	<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBI FirstGlance]. <br>
	</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [http://pdbe.org/5nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [http://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>		</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [http://pdbe.org/5nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [http://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Dym, O]]		[[Category: Dym, O]]
	[[Category: Fleishman, S J]]		[[Category: Fleishman, S J]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 06:56, 18 October 2017

2017-10-18T06:56:24Z

←Older revision		Revision as of 06:56, 18 October 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5nbi is ~~ON HOLD until Paper~~ Publication	+	==Principles for computational design of antibodies==
		+	<StructureSection load='5nbi' size='340' side='right' caption='[[5nbi]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBI FirstGlance]. <br>
		+	</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=5nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbi OCA], [http://pdbe.org/5nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbi RCSB], [http://www.ebi.ac.uk/pdbsum/5nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called "ideal" folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we (i) used sequence-design constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes.

-	~~Authors: Dym~~, O., ~~Fleishman~~, S.J.	+	Principles for computational design of binding antibodies.,Baran D, Pszolla MG, Lapidoth GD, Norn C, Dym O, Unger T, Albeck S, Tyka MD, Fleishman SJ Proc Natl Acad Sci U S A. 2017 Sep 25. pii: 201707171. doi:, 10.1073/pnas.1707171114. PMID:28973872<ref>PMID:28973872</ref>

-	~~Description: Principles for computational design~~ of ~~antibodies~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Fleishman, S.J]]~~	+	<div class="pdbe-citations 5nbi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Dym, O]]		[[Category: Dym, O]]
		+	[[Category: Fleishman, S J]]
		+	[[Category: Antibody]]
		+	[[Category: Immune system]]

OCA at 17:20, 15 March 2017

2017-03-15T17:20:42Z

←Older revision		Revision as of 17:20, 15 March 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5nbi is ON HOLD	+	The entry 5nbi is ON HOLD until Paper Publication

	Authors: Dym, O., Fleishman, S.J.		Authors: Dym, O., Fleishman, S.J.

OCA: Protected "5nbi" [edit=sysop:move=sysop]

2017-03-09T12:24:29Z

Protected "5nbi" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:24, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5nbi is ON HOLD Authors: Dym, O., Fleishman, S.J. Description: Principles for computational design of antibodies [[Category: Unreleased Structures]...

2017-03-09T12:24:27Z

New page: '''Unreleased structure''' The entry 5nbi is ON HOLD Authors: Dym, O., Fleishman, S.J. Description: Principles for computational design of antibodies [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 5nbi is ON HOLD

Authors: Dym, O., Fleishman, S.J.

Description: Principles for computational design of antibodies
[[Category: Unreleased Structures]]
[[Category: Fleishman, S.J]]
[[Category: Dym, O]]