7fbb - Revision history

OCA at 19:34, 29 May 2024

2024-05-29T19:34:31Z

← Older revision		Revision as of 19:34, 29 May 2024
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	<StructureSection load='7fbb' size='340' side='right'caption='[[7fbb]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='7fbb' size='340' side='right'caption='[[7fbb]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7fbb]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBB FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBB FirstGlance]. <br>
	</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=7fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbb OCA], [https://pdbe.org/7fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbb RCSB], [https://www.ebi.ac.uk/pdbsum/7fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbb 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]] 2.307Å</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=7fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbb OCA], [https://pdbe.org/7fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbb RCSB], [https://www.ebi.ac.uk/pdbsum/7fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbb ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[https://www.uniprot.org/uniprot/A0A4P1LXE0_SERSF A0A4P1LXE0_SERSF]] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	A protein backbone structure is designable if a substantial number of amino acid sequences exist that autonomously fold into it(1,2). It has been suggested that the designability of backbones is governed mainly by side chain-independent or side chain type-insensitive molecular interactions(3-5), indicating an approach for designing new backbones (ready for amino acid selection) based on continuous sampling and optimization of the backbone-centred energy surface. However, a sufficiently comprehensive and precise energy function has yet to be established for this purpose. Here we show that this goal is met by a statistical model named SCUBA (for Side Chain-Unknown Backbone Arrangement) that uses neural network-form energy terms. These terms are learned with a two-step approach that comprises kernel density estimation followed by neural network training and can analytically represent multidimensional, high-order correlations in known protein structures. We report the crystal structures of nine de novo proteins whose backbones were designed to high precision using SCUBA, four of which have novel, non-natural overall architectures. By eschewing use of fragments from existing protein structures, SCUBA-driven structure design facilitates far-reaching exploration of the designable backbone space, thus extending the novelty and diversity of the proteins amenable to de novo design.

	A backbone-centred energy function of neural networks for protein design.,Huang B, Xu Y, Hu X, Liu Y, Liao S, Zhang J, Huang C, Hong J, Chen Q, Liu H Nature. 2022 Feb;602(7897):523-528. doi: 10.1038/s41586-021-04383-5. Epub 2022, Feb 9. PMID:35140398<ref>PMID:35140398</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7fbb" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bin, H]]		[[Category: Bin H]]
	~~[[Category: De novo protein]]~~
	~~[[Category: Unknown function~~]]

OCA at 08:39, 23 February 2022

2022-02-23T08:39:10Z

@@ Line 8: / Line 8: @@
 == Function ==
 [[https://www.uniprot.org/uniprot/A0A4P1LXE0_SERSF A0A4P1LXE0_SERSF]] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005]
 __TOC__
 </StructureSection>

OCA at 10:59, 16 February 2022

2022-02-16T10:59:51Z

← Older revision		Revision as of 10:59, 16 February 2022
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	==De novo design protein D12 with MBP tag==		==De novo design protein D12 with MBP tag==
	<StructureSection load='7fbb' size='340' side='right'caption='[[7fbb]]' scene=''>		<StructureSection load='7fbb' size='340' side='right'caption='[[7fbb]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7fbb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBB FirstGlance]. <br>
	</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=7fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbb OCA], [https://pdbe.org/7fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbb RCSB], [https://www.ebi.ac.uk/pdbsum/7fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbb ProSAT]</span></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=7fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbb OCA], [https://pdbe.org/7fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbb RCSB], [https://www.ebi.ac.uk/pdbsum/7fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/A0A4P1LXE0_SERSF A0A4P1LXE0_SERSF]] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bin H]]		[[Category: Bin, H]]
			[[Category: De novo protein]]
			[[Category: Unknown function]]

OCA at 15:25, 22 December 2021

2021-12-22T15:25:32Z

← Older revision		Revision as of 15:25, 22 December 2021
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7fbb is ~~ON HOLD until Paper Publication~~		==De novo design protein D12 with MBP tag==
			<StructureSection load='7fbb' size='340' side='right'caption='[[7fbb]]' scene=''>
	~~Authors:~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBB FirstGlance]. <br>
	~~Description~~:		</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=7fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbb OCA], [https://pdbe.org/7fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbb RCSB], [https://www.ebi.ac.uk/pdbsum/7fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbb ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Bin H]]

OCA at 07:22, 8 September 2021

2021-09-08T07:22:24Z

← Older revision		Revision as of 07:22, 8 September 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7fbb is ON HOLD		The entry 7fbb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7fbb" [edit=sysop:move=sysop]

2021-07-14T08:44:18Z

Protected "7fbb" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:44, 14 July 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7fbb is ON HOLD Authors: Description: Category: Unreleased Structures

2021-07-14T08:44:17Z

New page: '''Unreleased structure''' The entry 7fbb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7fbb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]