Detection of unrealistic molecular environments in protein structures based on expect
Abstract Understanding the relationship between protein structure and biological function is a central theme in structural biology. Advances are severely hampered by errors in experimentally determined protein structures. Detection and correction of such errors is therefore of utmost importance. Electron densities in molecular structures obey certain rules which depend on the molecular environment. Here we present and discuss a new approach that relates electron densities computed from a structural model to densities expected from prior observations on identical or closely related molecular environments. Strong deviations of computed from expected densities reveal unrealistic molecular structures. Most importantly, structure analysis and error detection are independent of experimental data and hence may be applied to any structural model. The comparison to state-of-the-art methods reveals that our approach is able to identify errors that formerly remained undetected. The new technique, called RefDens, is accessible as a public web service at http://refdens.services.came.sbg.ac.at.
Content Type Journal Article
DOI 10.1007/s10858-010-9408-x
Authors
Simon W. Ginzinger, University of Salzburg Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering Hellbrunnerstr. 34 5020 Salzburg Austria
Christian X. Weichenberger, University of Salzburg Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering Hellbrunnerstr. 34 5020 Salzburg Austria
Manfred J. Sippl, University of Salzburg Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering Hellbrunnerstr. 34 5020 Salzburg Austria
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Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
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Abstract
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Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
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Detection of unrealistic molecular environments in protein structures based on expect
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