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2nr2

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Revision as of 09:07, 23 February 2022

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins

Structural highlights

2nr2 is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1xqq, 1d3z, 1ubq
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

While reliable procedures for determining the conformations of proteins are available, methods for generating ensembles of structures that also reflect their flexibility are much less well established. Here we present a systematic assessment of the ability of ensemble-averaged molecular dynamics simulations with ensemble-averaged NMR restraints to simultaneously reproduce the average structure of proteins and their associated dynamics. We discuss the effects that under-restraining (overfitting) and over-restraining (underfitting) have on the structures generated in ensemble-averaged molecular simulations. We then introduce the MUMO (minimal under-restraining minimal over-restraining) method, a procedure in which different observables are averaged over a different number of molecules. As both over-restraining and under-restraining are significantly reduced in the MUMO method, it is possible to generate ensembles of conformations that accurately characterize both the structure and the dynamics of native states of proteins. The application of the MUMO method to the protein ubiquitin yields a high-resolution structural ensemble with an RDC Q-factor of 0.19.

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins.,Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M J Biomol NMR. 2007 Feb;37(2):117-35. Epub 2007 Jan 16. PMID:17225069^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M. The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR. 2007 Feb;37(2):117-35. Epub 2007 Jan 16. PMID:17225069 doi:10.1007/s10858-006-9117-7

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2nr2"

@@ Line 3: / Line 3: @@
 <StructureSection load='2nr2' size='340' side='right'caption='[[2nr2]], [[NMR_Ensembles_of_Models | 144 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nr2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NR2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2NR2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nr2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NR2 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xqq|1xqq]], [[1d3z|1d3z]], [[1ubq|1ubq]]</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;'>[[1xqq|1xqq]], [[1d3z|1d3z]], [[1ubq|1ubq]]</div></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=2nr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nr2 OCA], [http://pdbe.org/2nr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nr2 RCSB], [http://www.ebi.ac.uk/pdbsum/2nr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2nr2 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=2nr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nr2 OCA], [https://pdbe.org/2nr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nr2 RCSB], [https://www.ebi.ac.uk/pdbsum/2nr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nr2 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 28: / Line 28: @@
 ==See Also==
-*[[Ubiquitin|Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>

2nr2

From Proteopedia

Revision as of 09:07, 23 February 2022

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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