Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies...
[NMR paper] The accuracy of protein structures in solution determined by AlphaFold and NMR
The accuracy of protein structures in solution determined by AlphaFold and NMR
AlphaFoldn the recent Critical Assessment of Structure Prediction (CASP) competition, AlphaFold2 performed outstandingly. Its worst predictions were for nuclear magnetic resonance (NMR) structures, which has two alternative explanations: either the NMR structures were poor, implying that Alpha-Fold may be more accurate than NMR, or there is a genuine difference between crystal and solution structures. Here, we use the program Accuracy of NMR Structures Using RCI and Rigidity (ANSURR), which...
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[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
J Am Chem Soc. 2014 Jan 6;
Authors: Mao B, Tejero R, Baker D, Montelione GT
Abstract
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...
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01-08-2014 11:23 AM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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02-11-2012 10:31 AM
[NMR paper] Improving the accuracy of NMR structures of large proteins using pseudocontact shifts
Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints.
Related Articles Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints.
J Biomol NMR. 2004 Mar;28(3):205-12
Authors: Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J, Byrd RA
We demonstrate improved accuracy in protein structure determination for large (>/=30 kDa), deuterated proteins (e.g. STAT4(NT)) via the combination of pseudocontact shifts for amide and methyl protons...
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11-24-2010 09:25 PM
Multidomain Protein Structures from NMR & Solution Small-Angle X-ray Scattering
http://pubs.acs.org/isubscribe/journals/jacsat/127/i47/figures/ja054342mn00001.gif
Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data
Alexander Grishaev,* Justin Wu, Jill Trewhella, and Ad Bax*
Contribution from the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
J. Am. Chem. Soc.; 2005; 127(47) pp 16621 -...
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures
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