5up5 - Revision history

OCA at 10:26, 14 June 2023

OCA — Wed, 14 Jun 2023 10:26:50 GMT

←Older revision		Revision as of 10:26, 14 June 2023
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	==Solution structure of the de novo mini protein EHEE_rd1_0284==		==Solution structure of the de novo mini protein EHEE_rd1_0284==
-	<StructureSection load='5up5' size='340' side='right'caption='[[5up5~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5up5' size='340' side='right'caption='[[5up5]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5up5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UP5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UP5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5up5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UP5 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uoi\|5uoi]], [[5up1\|5up1]]</td></tr>~~	+	</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=5up5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5up5 OCA], [https://pdbe.org/5up5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5up5 RCSB], [https://www.ebi.ac.uk/pdbsum/5up5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5up5 ProSAT]</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=5up5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5up5 OCA], [~~http~~://pdbe.org/5up5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5up5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5up5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5up5 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: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Carter, L]]	+	[[Category: Carter L]]
-	[[Category: Chidyausiku~~, T M~~]]	+	[[Category: Chidyausiku TM]]
-	[[Category: Houliston, S]]	+	[[Category: Houliston S]]
-	[[Category: Lemak, A]]	+	[[Category: Lemak A]]
-	[[Category: Rocklin~~, G J]]~~	+	[[Category: Rocklin GJ]]
-	~~[[Category: De novo design]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Mini protein~~]]	+

OCA at 08:23, 8 January 2020

OCA — Wed, 08 Jan 2020 08:23:20 GMT

←Older revision		Revision as of 08:23, 8 January 2020
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	==Solution structure of the de novo mini protein EHEE_rd1_0284==		==Solution structure of the de novo mini protein EHEE_rd1_0284==
-	<StructureSection load='5up5' size='340' side='right' caption='[[5up5]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5up5' size='340' side='right'caption='[[5up5]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5up5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UP5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UP5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5up5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UP5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UP5 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 04:51, 16 November 2017

OCA — Thu, 16 Nov 2017 04:51:29 GMT

←Older revision		Revision as of 04:51, 16 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5up5 is ~~ON HOLD until Paper~~ Publication	+	==Solution structure of the de novo mini protein EHEE_rd1_0284==
		+	<StructureSection load='5up5' size='340' side='right' caption='[[5up5]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5up5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UP5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UP5 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uoi\|5uoi]], [[5up1\|5up1]]</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=5up5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5up5 OCA], [http://pdbe.org/5up5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5up5 RCSB], [http://www.ebi.ac.uk/pdbsum/5up5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5up5 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.

-	~~Authors: Houliston~~, S., Rocklin, ~~G.J.~~, ~~Lemak~~, A., ~~Carter~~, L., ~~Chidyausiku~~, ~~T.M.~~, ~~Baker, D.~~, Arrowsmith, C.H.	+	Global analysis of protein folding using massively parallel design, synthesis, and testing.,Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D Science. 2017 Jul 14;357(6347):168-175. doi: 10.1126/science.aan0693. PMID:28706065<ref>PMID:28706065</ref>

-	~~Description: Solution structure~~ of the ~~de novo mini protein EHEE_rd1_0284~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5up5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Arrowsmith, C H]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
-	[[Category: Chidyausiku, T.M]]
-	[[Category: Rocklin, G.J]]
-	[[Category: Lemak, A]]
-	[[Category: Arrowsmith, C.H]]
-	[[Category: Houliston, S]]
	[[Category: Carter, L]]		[[Category: Carter, L]]
		+	[[Category: Chidyausiku, T M]]
		+	[[Category: Houliston, S]]
		+	[[Category: Lemak, A]]
		+	[[Category: Rocklin, G J]]
		+	[[Category: De novo design]]
		+	[[Category: De novo protein]]
		+	[[Category: Mini protein]]

OCA at 10:42, 4 May 2017

OCA — Thu, 04 May 2017 10:42:44 GMT

←Older revision		Revision as of 10:42, 4 May 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5up5 is ON HOLD	+	The entry 5up5 is ON HOLD until Paper Publication

	Authors: Houliston, S., Rocklin, G.J., Lemak, A., Carter, L., Chidyausiku, T.M., Baker, D., Arrowsmith, C.H.		Authors: Houliston, S., Rocklin, G.J., Lemak, A., Carter, L., Chidyausiku, T.M., Baker, D., Arrowsmith, C.H.

OCA at 19:15, 15 March 2017

OCA — Wed, 15 Mar 2017 19:15:46 GMT

←Older revision		Revision as of 19:15, 15 March 2017
Line 7:		Line 7:
	Description: Solution structure of the de novo mini protein EHEE_rd1_0284		Description: Solution structure of the de novo mini protein EHEE_rd1_0284
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Houliston, S]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Chidyausiku, T.M]]		[[Category: Chidyausiku, T.M]]
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	[[Category: Lemak, A]]		[[Category: Lemak, A]]
	[[Category: Arrowsmith, C.H]]		[[Category: Arrowsmith, C.H]]
		+	[[Category: Houliston, S]]
	[[Category: Carter, L]]		[[Category: Carter, L]]

OCA: Protected "5up5" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 14:45:24 GMT

Protected "5up5" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:45, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5up5 is ON HOLD Authors: Houliston, S., Rocklin, G.J., Lemak, A., Carter, L., Chidyausiku, T.M., Baker, D., Arrowsmith, C.H. Description: Solution ...

OCA — Thu, 09 Mar 2017 14:45:22 GMT

New page: '''Unreleased structure''' The entry 5up5 is ON HOLD Authors: Houliston, S., Rocklin, G.J., Lemak, A., Carter, L., Chidyausiku, T.M., Baker, D., Arrowsmith, C.H. Description: Solution ...

New page

'''Unreleased structure'''

The entry 5up5 is ON HOLD

Authors: Houliston, S., Rocklin, G.J., Lemak, A., Carter, L., Chidyausiku, T.M., Baker, D., Arrowsmith, C.H.

Description: Solution structure of the de novo mini protein EHEE_rd1_0284
[[Category: Unreleased Structures]]
[[Category: Houliston, S]]
[[Category: Baker, D]]
[[Category: Chidyausiku, T.M]]
[[Category: Rocklin, G.J]]
[[Category: Lemak, A]]
[[Category: Arrowsmith, C.H]]
[[Category: Carter, L]]