7mcd - Revision history

OCA at 07:18, 3 April 2024

2024-04-03T07:18:54Z

← Older revision		Revision as of 07:18, 3 April 2024
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	<StructureSection load='7mcd' size='340' side='right'caption='[[7mcd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='7mcd' size='340' side='right'caption='[[7mcd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7mcd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7mcd]] is a 4 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=7MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MCD FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~7mcc~~\|~~7mcc~~]]~~</div>~~</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]] 1.9Å</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=7mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mcd OCA], [https://pdbe.org/7mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mcd RCSB], [https://www.ebi.ac.uk/pdbsum/7mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mcd 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=7mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mcd OCA], [https://pdbe.org/7mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mcd RCSB], [https://www.ebi.ac.uk/pdbsum/7mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mcd ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

	Protein sequence design with a learned potential.,Anand N, Eguchi R, Mathews II, Perez CP, Derry A, Altman RB, Huang PS Nat Commun. 2022 Feb 8;13(1):746. doi: 10.1038/s41467-022-28313-9. PMID:35136054<ref>PMID:35136054</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7mcd" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Anand-Achim, N]]		[[Category: Synthetic construct]]
	[[Category: Huang, P]]		[[Category: Anand-Achim N]]
	[[Category: Mathews~~, I I~~]]		[[Category: Huang P]]
	[[Category: Perez~~, C P]]~~		[[Category: Mathews II]]
	~~[[Category: De novo protein]]~~		[[Category: Perez CP]]
	~~[[Category: Tim-barrel~~]]

OCA at 08:41, 23 February 2022

2022-02-23T08:41:05Z

← Older revision		Revision as of 08:41, 23 February 2022
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	==Crystal structure of an AI-designed TIM-barrel F15C==		==Crystal structure of an AI-designed TIM-barrel F15C==
	<StructureSection load='7mcd' size='340' side='right'caption='[[7mcd]]' scene=''>		<StructureSection load='7mcd' size='340' side='right'caption='[[7mcd]], [[Resolution\|resolution]] 1.90Å' 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=7MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7mcd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MCD 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=7mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mcd OCA], [https://pdbe.org/7mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mcd RCSB], [https://www.ebi.ac.uk/pdbsum/7mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mcd ProSAT]</span></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7mcc\|7mcc]]</div></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=7mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mcd OCA], [https://pdbe.org/7mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mcd RCSB], [https://www.ebi.ac.uk/pdbsum/7mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mcd ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

			Protein sequence design with a learned potential.,Anand N, Eguchi R, Mathews II, Perez CP, Derry A, Altman RB, Huang PS Nat Commun. 2022 Feb 8;13(1):746. doi: 10.1038/s41467-022-28313-9. PMID:35136054<ref>PMID:35136054</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7mcd" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Anand-Achim N]]		[[Category: Anand-Achim, N]]
	[[Category: Huang P]]		[[Category: Huang, P]]
	[[Category: Mathews II]]		[[Category: Mathews, I I]]
	[[Category: Perez CP]]		[[Category: Perez, C P]]
			[[Category: De novo protein]]
			[[Category: Tim-barrel]]

OCA at 07:29, 19 January 2022

2022-01-19T07:29:07Z

← Older revision		Revision as of 07:29, 19 January 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7mcd is ~~ON HOLD~~		==Crystal structure of an AI-designed TIM-barrel F15C==
			<StructureSection load='7mcd' size='340' side='right'caption='[[7mcd]]' scene=''>
	~~Authors~~: ~~Mathews~~, I.I.~~, Anand~~-~~Achim~~, N., ~~Perez~~, C.P., ~~Huang, P~~.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MCD FirstGlance]. <br>
	~~Description: Crystal structure of an AI-designed TIM-barrel F15C~~		</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=7mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mcd OCA], [https://pdbe.org/7mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mcd RCSB], [https://www.ebi.ac.uk/pdbsum/7mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mcd ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Mathews, I.I~~]]		__TOC__
	[[Category: Huang, P]]		</StructureSection>
	[[Category: ~~Perez, C.P~~]]		[[Category: Large Structures]]
	[[Category: ~~Anand-Achim, N~~]]		[[Category: Anand-Achim N]]
			[[Category: Huang P]]
			[[Category: Mathews II]]
			[[Category: Perez CP]]

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

2021-04-07T04:44:07Z

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

← Older revision	Revision as of 04:44, 7 April 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7mcd is ON HOLD Authors: Mathews, I.I., Anand-Achim, N., Perez, C.P., Huang, P. Description: Crystal structure of an AI-designed TIM-barrel F15C [[...

2021-04-07T04:44:06Z

New page: '''Unreleased structure''' The entry 7mcd is ON HOLD Authors: Mathews, I.I., Anand-Achim, N., Perez, C.P., Huang, P. Description: Crystal structure of an AI-designed TIM-barrel F15C [[...

New page

'''Unreleased structure'''

The entry 7mcd is ON HOLD

Authors: Mathews, I.I., Anand-Achim, N., Perez, C.P., Huang, P.

Description: Crystal structure of an AI-designed TIM-barrel F15C
[[Category: Unreleased Structures]]
[[Category: Mathews, I.I]]
[[Category: Huang, P]]
[[Category: Perez, C.P]]
[[Category: Anand-Achim, N]]