NMRPipe: A multidimensional spectral processing system based on UNIX pipes
- F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, John Pfeifer, A. Bax
- Computer ScienceJournal of Biomolecular NMR
- 30 October 1995
The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
Protein backbone angle restraints from searching a database for chemical shift and sequence homology
TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence, and these averages can reliably be used as angular restraints for the protein whose structure is being studied.
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
- Yang Shen, F. Delaglio, Gabriel Cornilescu, A. Bax
- Biology, ChemistryJournal of Biomolecular NMR
- 23 June 2009
Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%, and addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%.
MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy
Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase
The change in chemical shift ( ∆δ) observed for a given nucleus, when shifting from an isotropic medium to a strongly oriented, liquid crystalline phase, contains valuable information on the…
Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease.
The use of novel two-dimensional nuclear magnetic resonance (NMR) pulse sequences to provide insight into protein dynamics is described, suggesting that there is no correlation between these rapid small amplitude motions and secondary structure for S. Nase.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks
Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, and an acceptance criterion that is nearly two-fold tighter than that used previously.
Consistent blind protein structure generation from NMR chemical shift data
- Yang Shen, O. Lange, A. Bax
- Biology, ChemistryProceedings of the National Academy of Sciences
- 25 March 2008
The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods, and potentially provides a new direction for high-throughput NMR structure determination.
Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium.
The approach promises to improve the accuracy of structures determined by NMR, and extend the size limit, and distances and angles derived from dipolar couplings in human ubiquitin are in excellent agreement with its crystal structure.
Solution structure of a calmodulin-target peptide complex by multidimensional NMR.
The three-dimensional solution structure of the complex between calcium-bound calmodulin (Ca(2+)-CaM) and a 26-residue synthetic peptide comprising the CaM binding domain (residues 577 to 602) of…