6be9 - Revision history

OCA at 10:37, 14 June 2023

2023-06-14T10:37:57Z

←Older revision		Revision as of 10:37, 14 June 2023
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	==Solution structure of de novo macrocycle design7.1==		==Solution structure of de novo macrocycle design7.1==
-	<StructureSection load='6be9' size='340' side='right'caption='[[6be9~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6be9' size='340' side='right'caption='[[6be9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6be9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BE9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6be9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BE9 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6be9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6be9 OCA], [~~http~~://pdbe.org/6be9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6be9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6be9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6be9 ProSAT]</span></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=6be9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6be9 OCA], [https://pdbe.org/6be9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6be9 RCSB], [https://www.ebi.ac.uk/pdbsum/6be9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6be9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baker, B]]	+	[[Category: Baker B]]
-	[[Category: Hosseinzadeh, P]]	+	[[Category: Hosseinzadeh P]]
-	[[Category: Pardo-Avila, F]]	+	[[Category: Pardo-Avila F]]
-	[[Category: Shortridge~~, M D~~]]	+	[[Category: Shortridge MD]]
-	[[Category: Varani, G]]	+	[[Category: Varani G]]
-	~~[[Category: De novo]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Macrocycle~~]]	+

OCA at 08:49, 11 November 2020

2020-11-11T08:49:07Z

←Older revision		Revision as of 08:49, 11 November 2020
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	==Solution structure of de novo macrocycle design7.1==		==Solution structure of de novo macrocycle design7.1==
-	<StructureSection load='6be9' size='340' side='right' caption='[[6be9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6be9' size='340' side='right'caption='[[6be9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6be9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BE9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6be9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BE9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BE9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</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=6be9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6be9 OCA], [http://pdbe.org/6be9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6be9 RCSB], [http://www.ebi.ac.uk/pdbsum/6be9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6be9 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6be9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6be9 OCA], [http://pdbe.org/6be9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6be9 RCSB], [http://www.ebi.ac.uk/pdbsum/6be9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6be9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baker, B]]		[[Category: Baker, B]]
	[[Category: Hosseinzadeh, P]]		[[Category: Hosseinzadeh, P]]

OCA at 08:38, 27 December 2017

2017-12-27T08:38:19Z

←Older revision		Revision as of 08:38, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6be9 is ~~ON HOLD~~	+	==Solution structure of de novo macrocycle design7.1==
		+	<StructureSection load='6be9' size='340' side='right' caption='[[6be9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6be9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BE9 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</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=6be9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6be9 OCA], [http://pdbe.org/6be9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6be9 RCSB], [http://www.ebi.ac.uk/pdbsum/6be9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6be9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

-	~~Authors: Shortridge, M.D~~., Hosseinzadeh, P., Pardo-Avila, F., ~~Varani~~, G., Baker~~, B~~.	+	Comprehensive computational design of ordered peptide macrocycles.,Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D Science. 2017 Dec 15;358(6369):1461-1466. doi: 10.1126/science.aap7577. PMID:29242347<ref>PMID:29242347</ref>

-	~~Description: Solution structure~~ of ~~de novo macrocycle design7~~.1	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Varani, G]]~~	+	<div class="pdbe-citations 6be9" style="background-color:#fffaf0;"></div>
-	~~[[Category: Pardo-Avila, F]]~~	+	== References ==
-	~~[[Category: Shortridge, M.D]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Baker, B]]		[[Category: Baker, B]]
	[[Category: Hosseinzadeh, P]]		[[Category: Hosseinzadeh, P]]
		+	[[Category: Pardo-Avila, F]]
		+	[[Category: Shortridge, M D]]
		+	[[Category: Varani, G]]
		+	[[Category: De novo]]
		+	[[Category: De novo protein]]
		+	[[Category: Macrocycle]]

OCA: Protected "6be9" [edit=sysop:move=sysop]

2017-11-01T04:59:12Z

Protected "6be9" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 6be9 is ON HOLD Authors: Shortridge, M.D., Hosseinzadeh, P., Pardo-Avila, F., Varani, G., Baker, B. Description: Solution structure of de novo macr...

2017-11-01T04:59:11Z

New page: '''Unreleased structure''' The entry 6be9 is ON HOLD Authors: Shortridge, M.D., Hosseinzadeh, P., Pardo-Avila, F., Varani, G., Baker, B. Description: Solution structure of de novo macr...

New page

'''Unreleased structure'''

The entry 6be9 is ON HOLD

Authors: Shortridge, M.D., Hosseinzadeh, P., Pardo-Avila, F., Varani, G., Baker, B.

Description: Solution structure of de novo macrocycle design7.1
[[Category: Unreleased Structures]]
[[Category: Varani, G]]
[[Category: Pardo-Avila, F]]
[[Category: Shortridge, M.D]]
[[Category: Baker, B]]
[[Category: Hosseinzadeh, P]]