2nr2: Difference between revisions
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==The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins== | ==The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins== | ||
<StructureSection load='2nr2' size='340' side='right' caption='[[2nr2]], [[NMR_Ensembles_of_Models | 144 NMR models]]' scene=''> | <StructureSection load='2nr2' size='340' side='right'caption='[[2nr2]], [[NMR_Ensembles_of_Models | 144 NMR models]]' scene=''> | ||
== Structural highlights == | == 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:// | <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> | ||
</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">[[1xqq|1xqq]], [[1d3z|1d3z]], [[1ubq|1ubq]]</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <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> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Human]] | [[Category: Human]] | ||
[[Category: Large Structures]] | |||
[[Category: Gsponer, J]] | [[Category: Gsponer, J]] | ||
[[Category: Richter, B]] | [[Category: Richter, B]] | ||
Revision as of 09:34, 20 May 2020
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteinsThe MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins
Structural highlights
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 PubMedWhile 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. See AlsoReferences
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