The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMRâ??from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
[NMR paper] Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints.
Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints.
Related Articles Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints.
Curr Opin Struct Biol. 2014 Feb;24C:45-53
Authors: Hass MA, Ubbink M
Abstract
Paramagnetic NMR spectroscopy has evolved rapidly in the last decade, and has shown to be a very useful tool for solving structures of protein-protein complexes. A major breakthrough has been the development of...
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04-12-2014 06:36 PM
Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints
Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints
Publication date: February 2014
Source:Current Opinion in Structural Biology, Volume 24</br>
Author(s): Mathias AS Hass , Marcellus Ubbink</br>
Paramagnetic NMR spectroscopy has evolved rapidly in the last decade, and has shown to be a very useful tool for solving structures of protein–protein complexes. A major breakthrough has been the development of paramagnetic metal binding tags that can be attached specifically to the protein. These tags have greatly...
[NMR paper] Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils.
Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils.
Related Articles Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils.
Annu Rev Biophys. 2013 Mar 22;
Authors: Comellas G, Rienstra CM
Abstract
Protein structure determination methods using magic-angle spinning solidstate nuclear magnetic resonance (MAS SSNMR) have experienced a remarkable...
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03-27-2013 03:33 PM
Parameterization of Solvent-Protein Interaction and Its Use on NMR Protein Structure Determination
Parameterization of Solvent-Protein Interaction and Its Use on NMR Protein Structure Determination
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Yu Wang, Charles D. Schwieters, Nico Tjandra</br>
NMR structure determination is frequently hindered by an insufficient amount of distance information for determining the correct fold of the protein in its early stages. In response we introduce a simple and general structure-based metric that can be used to incorporate NMR-based restraints on protein surface accessibility. This metric is inversely...
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06-07-2012 06:58 AM
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Structure. 2010 Dec 8;18(12):1678-1687
Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ
Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...
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12-08-2010 06:21 PM
NMRFAM Workshop: NMR data collection and analysis for biological structure determination
NMRFAM Workshop: NMR data collection and analysis for biological structure determination
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The NMR facility is pleased to announce its first NMRFAM workshop to be held from noon June 6 through noon June 9, 2006 in the Biochemistry Addition at the University of Wisconsin-Madison.
The detailed program for the workshop is now available.
Purpose This workshop will offer a unique opportunity for participants to experience a combination of hands-on computational sessions, presentations, and discussions focusing on recently developed tools as well as emerging methods in NMR data...
NMRFAM-SDF: a protein structure determination framework
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