Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects. Finally, the different available force fields are presented, among other Xplor-NIH capabilities. This article is protected by copyright. All rights reserved.
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
Abstract
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from...
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05-13-2016 09:30 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] NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
J Biomol NMR. 2015 Mar 4;
Authors: Jang R, Wang Y, Xue Z, Zhang Y
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second...
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03-06-2015 12:45 AM
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements....
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03-04-2015 08:56 AM
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Publication date: Available online 3 April 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Charles D. Schwieters , G. Marius Clore</br>
This contribution describes the use of small and wide angle X-ray and small angle neutron scattering for biomolecular structure calculation using the program Xplor-NIH, both with and without NMR data. The current algorithms used for calculating scattering curves are described, and the use of scattering data as a...
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04-04-2014 01:19 PM
[NMR paper] An algebraic geometry approach to protein structure determination from NMR data.
An algebraic geometry approach to protein structure determination from NMR data.
Related Articles An algebraic geometry approach to protein structure determination from NMR data.
Proc IEEE Comput Syst Bioinform Conf. 2005;:235-46
Authors: Wang L, Mettu RR, Donald BR
Our paper describes the first provably-efficient algorithm for determining protein structures de novo, solely from experimental data. We show how the global nature of a certain kind of NMR data provides quantifiable complexity-theoretic benefits, allowing us to classify our...
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11-24-2010 11:14 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...
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11-19-2010 08:29 PM
[NMR paper] A systematic comparison of three structure determination methods from NMR data: depen
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
Related Articles A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
J Biomol NMR. 1992 Jul;2(4):373-88
Authors: Liu Y, Zhao D, Altman R, Jardetzky O
We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...
Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources
Linear Mode
