Related ArticlesStructure modeling of RNA using sparse NMR constraints.
Nucleic Acids Res. 2017 Dec 15;45(22):12638-12647
Authors: Williams B, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV
Abstract
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs.
[NMR paper] 3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.
3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.
3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.
Methods Mol Biol. 2017;1526:3-21
Authors: Pilla KB, Otting G, Huber T
Abstract
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR)...
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11-30-2016 11:16 AM
Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data
Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data
Publication date: 16 February 2016
Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br>
Author(s): Justin L. MacCallum, Yuefeng Tang, Y. Janet Huang, Gaetano T. Montelione</br>
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02-17-2016 07:50 PM
[NMR paper] Sparse labeling of proteins: Structural characterization from long range constraints
Sparse labeling of proteins: Structural characterization from long range constraints
Publication date: April 2014
Source:Journal of Magnetic Resonance, Volume 241</br>
Author(s): James H. Prestegard , David A. Agard , Kelley W. Moremen , Laura A. Lavery , Laura C. Morris , Kari Pederson</br>
Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In...
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology]
Protein structure modeling using sparse NMR data
Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D....
Date: 2012-06-19
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...
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06-20-2012 02:28 AM
[NMR paper] TOUCHSTONEX: protein structure prediction with sparse NMR data.
TOUCHSTONEX: protein structure prediction with sparse NMR data.
Related Articles TOUCHSTONEX: protein structure prediction with sparse NMR data.
Proteins. 2003 Nov 1;53(2):290-306
Authors: Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J
TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly...
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11-24-2010 09:16 PM
[NMR paper] An easy way to include weak alignment constraints into NMR structure calculations.
An easy way to include weak alignment constraints into NMR structure calculations.
Related Articles An easy way to include weak alignment constraints into NMR structure calculations.
J Biomol NMR. 2001 Nov;21(3):275-80
Authors: Sass HJ, Musco G, Stahl SJ, Wingfield PT, Grzesiek S
We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek. J. Biomol. NMR, 1999, 15,...
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11-19-2010 08:44 PM
[NMR paper] De novo protein structure determination using sparse NMR data.
De novo protein structure determination using sparse NMR data.
Related Articles De novo protein structure determination using sparse NMR data.
J Biomol NMR. 2000 Dec;18(4):311-8
Authors: Bowers PM, Strauss CE, Baker D
We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...
Structure modeling of RNA using sparse NMR constraints.
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