4nvb - Revision history

OCA at 12:35, 1 March 2024

2024-03-01T12:35:38Z

←Older revision		Revision as of 12:35, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_RM11-1a Saccharomyces cerevisiae RM11-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_RM11-1a Saccharomyces cerevisiae RM11-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NVB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25T:2-AMINO-5-METHYLTHIAZOLE'>25T</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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]] 1.17Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25T:2-AMINO-5-METHYLTHIAZOLE'>25T</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [https://pdbe.org/4nvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [https://www.ebi.ac.uk/pdbsum/4nvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvb 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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [https://pdbe.org/4nvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [https://www.ebi.ac.uk/pdbsum/4nvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]		[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.
-
-	Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.,Fischer M, Coleman RG, Fraser JS, Shoichet BK Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25. PMID:24950326<ref>PMID:24950326</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4nvb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]		*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:42, 18 January 2023

2023-01-18T08:42:03Z

←Older revision		Revision as of 08:42, 18 January 2023
Line 1:		Line 1:

	==Predicting protein conformational response in prospective ligand discovery.==		==Predicting protein conformational response in prospective ligand discovery.==
-	<StructureSection load='4nvb' size='340' side='right' caption='[[4nvb]], [[Resolution\|resolution]] 1.17Å' scene=''>	+	<StructureSection load='4nvb' size='340' side='right'caption='[[4nvb]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nvb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NVB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_RM11-1a Saccharomyces cerevisiae RM11-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NVB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=25T:2-AMINO-5-METHYLTHIAZOLE'>25T</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25T:2-AMINO-5-METHYLTHIAZOLE'>25T</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nva\|4nva]], [[4nvc\|4nvc]], [[4nvd\|4nvd]], [[4nve\|4nve]], [[4nvf\|4nvf]], [[4nvg\|4nvg]], [[4nvh\|4nvh]], [[4nvi\|4nvi]], [[4nvj\|4nvj]], [[4nvk\|4nvk]], [[4nvl\|4nvl]], [[4nvm\|4nvm]], [[4nvn\|4nvn]], [[4nvo\|4nvo]]</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [https://pdbe.org/4nvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [https://www.ebi.ac.uk/pdbsum/4nvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvb ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [~~http~~://pdbe.org/4nvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]	+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fischer, M~~]]	+	[[Category: Saccharomyces cerevisiae RM11-1a]]
-	[[Category: ~~Fraser, J S~~]]	+	[[Category: Fischer M]]
-	[[Category: ~~Boltzmann weight]]~~	+	[[Category: Fraser JS]]
-	~~[[Category: Dynamic]]~~	+
-	~~[[Category: Energy penalty]]~~	+
-	~~[[Category: Flexibility]]~~	+
-	~~[[Category: Flexible docking]]~~	+
-	~~[[Category: Ligand binding]]~~	+
-	~~[[Category: Loop]]~~	+
-	~~[[Category: Model system]]~~	+
-	~~[[Category: Occupancy]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Side-chain~~]]	+

OCA at 14:23, 29 March 2017

2017-03-29T14:23:31Z

←Older revision		Revision as of 14:23, 29 March 2017
Line 1:		Line 1:
		+
	==Predicting protein conformational response in prospective ligand discovery.==		==Predicting protein conformational response in prospective ligand discovery.==
	<StructureSection load='4nvb' size='340' side='right' caption='[[4nvb]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='4nvb' size='340' side='right' caption='[[4nvb]], [[Resolution\|resolution]] 1.17Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nva\|4nva]], [[4nvc\|4nvc]], [[4nvd\|4nvd]], [[4nve\|4nve]], [[4nvf\|4nvf]], [[4nvg\|4nvg]], [[4nvh\|4nvh]], [[4nvi\|4nvi]], [[4nvj\|4nvj]], [[4nvk\|4nvk]], [[4nvl\|4nvl]], [[4nvm\|4nvm]], [[4nvn\|4nvn]], [[4nvo\|4nvo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nva\|4nva]], [[4nvc\|4nvc]], [[4nvd\|4nvd]], [[4nve\|4nve]], [[4nvf\|4nvf]], [[4nvg\|4nvg]], [[4nvh\|4nvh]], [[4nvi\|4nvi]], [[4nvj\|4nvj]], [[4nvk\|4nvk]], [[4nvl\|4nvl]], [[4nvm\|4nvm]], [[4nvn\|4nvn]], [[4nvo\|4nvo]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [http://www.ebi.ac.uk/pdbsum/4nvb PDBsum]</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [http://pdbe.org/4nvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [http://www.ebi.ac.uk/pdbsum/4nvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4nvb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 06:48, 24 June 2015

2015-06-24T06:48:53Z

←Older revision		Revision as of 06:48, 24 June 2015
Line 8:		Line 8:
	<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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [http://www.ebi.ac.uk/pdbsum/4nvb PDBsum]</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [http://www.ebi.ac.uk/pdbsum/4nvb PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.
		+
		+	Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.,Fischer M, Coleman RG, Fraser JS, Shoichet BK Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25. PMID:24950326<ref>PMID:24950326</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:26, 21 December 2014

2014-12-21T17:26:49Z

←Older revision		Revision as of 17:26, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nvb\| PDB=4nvb \| SCENE= }}~~	+	==Predicting protein conformational response in prospective ligand discovery.==
-	===Predicting protein conformational response in prospective ligand discovery.===	+	<StructureSection load='4nvb' size='340' side='right' caption='[[4nvb]], [[Resolution\|resolution]] 1.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4nvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NVB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=25T:2-AMINO-5-METHYLTHIAZOLE'>25T</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nva\|4nva]], [[4nvc\|4nvc]], [[4nvd\|4nvd]], [[4nve\|4nve]], [[4nvf\|4nvf]], [[4nvg\|4nvg]], [[4nvh\|4nvh]], [[4nvi\|4nvi]], [[4nvj\|4nvj]], [[4nvk\|4nvk]], [[4nvl\|4nvl]], [[4nvm\|4nvm]], [[4nvn\|4nvn]], [[4nvo\|4nvo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</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=4nvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nvb RCSB], [http://www.ebi.ac.uk/pdbsum/4nvb PDBsum]</span></td></tr>
		+	</table>

-	==~~About this Structure~~==	+	==See Also==
-	[[~~4nvb~~]] ~~is a 1 chain structure. Full crystallographic information is available from~~ [~~http~~:~~//oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA~~].	+	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
-	[[Category: Fischer, M.]]	+	__TOC__
-	[[Category: Fraser, J S.]]	+	</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Fischer, M]]
		+	[[Category: Fraser, J S]]
	[[Category: Boltzmann weight]]		[[Category: Boltzmann weight]]
	[[Category: Dynamic]]		[[Category: Dynamic]]

OCA at 10:44, 18 December 2013

2013-12-18T10:44:58Z

←Older revision		Revision as of 10:44, 18 December 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4nvb\| PDB=4nvb \| SCENE= }}
		+	===Predicting protein conformational response in prospective ligand discovery.===

-	~~The entry~~ 4nvb is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4nvb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NVB OCA].
-	~~Authors~~: Fischer, M., Fraser, J.S.	+	[[Category: Fischer, M.]]
-		+	[[Category: Fraser, J S.]]
-	~~Description~~: ~~Predicting protein conformational response in prospective ligand discovery.~~	+	[[Category: Boltzmann weight]]
		+	[[Category: Dynamic]]
		+	[[Category: Energy penalty]]
		+	[[Category: Flexibility]]
		+	[[Category: Flexible docking]]
		+	[[Category: Ligand binding]]
		+	[[Category: Loop]]
		+	[[Category: Model system]]
		+	[[Category: Occupancy]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Side-chain]]

OCA: Protected "4nvb" [edit=sysop:move=sysop]

2013-12-11T13:09:47Z

Protected "4nvb" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:09, 11 December 2013

OCA: New page: '''Unreleased structure''' The entry 4nvb is ON HOLD Authors: Fischer, M., Fraser, J.S. Description: Predicting protein conformational response in prospective ligand discovery.

2013-12-11T13:09:46Z

New page: '''Unreleased structure''' The entry 4nvb is ON HOLD Authors: Fischer, M., Fraser, J.S. Description: Predicting protein conformational response in prospective ligand discovery.

New page

'''Unreleased structure'''

The entry 4nvb is ON HOLD

Authors: Fischer, M., Fraser, J.S.

Description: Predicting protein conformational response in prospective ligand discovery.