ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2012
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.The Journal of biological chemistry · 2019Article
- Applications of NMR to membrane proteins.Archives of biochemistry and biophysics · 2017Review
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.Biophysical journal · 2015Article
- Structure of the membrane protein MerF, a bacterial mercury transporter, improved by the inclusion of chemical shift anisotropy constraints.Journal of biomolecular NMR · 2014Article
- NMR structures of membrane proteins in phospholipid bilayers.Quarterly reviews of biophysics · 2014Review
- Sparse labeling of proteins: structural characterization from long range constraints.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Review
- High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion.Journal of the American Chemical Society · 2014Article
- Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR.Journal of biomolecular NMR · 2014Article
- Membrane protein structure determination in membrana.Accounts of chemical research · 2013Article
- NMR-based simulation studies of Pf1 coat protein in explicit membranes.Biophysical journal · 2013Article
- Membrane protein structure determination: back to the membrane.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.Protein science : a publication of the Protein Society · 2012Article
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Authors and funding
4 authors.
Funding
Abstract
AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.
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