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Publications for SHIFTX
Combined 1H Detected Solid State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments
[…] . Spectra were referenced against adamantane () and histidine () powders. Data were processed with TopSpin 3.0 (Bruker Biospin) and analyzed using Sparky (). Chemical shift predictions were made with Shiftx2 () and FANDAS () using atomic model PDB ID 3wvf (). […]
Quenching protein dynamics interferes with HIV capsid maturation
[…] MHR were observed.Fig. 4 In order to gain a quantitative understanding of the experimental isotropic MAS frequencies of CA–SP1 assemblies, chemical shifts were calculated with the data-based program SHIFTX2 for every MD frame and each of the six WT CTD–SP1 chains. Averaging the shifts for the MD trajectory over all frames and all chains of the hexamer yielded excellent agreement between calculate […]
A new role for FBP21 as regulator of Brr2 helicase activity
[…] ement time. Assignment of the HSQC signals was accomplished using CCPNMR Analysis 2.2.2 () and chemical shift predictions derived from the crystal structure of Brr2C-Sec63 (part of PDB ID 4F91) using ShiftX2 (). All 1H–15N-TROSY-HSQC spectra of amino acid-selectively labeled Brr2C-Sec63 (Leu, Ala (-Trp), Ile, Val, Gly (–Ser, –Cys), Trp–Tyr, Tyr–Phe) were measured at 100–300 μM in 10 mM sodium phos […]
Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists
[…] size or chemical exchange processes . As an alternative approach, dihedral angles and the secondary structure of proteins are predicted by the programs TALOS (and related versions) , , CamShift and SHIFTX2 . These programs use prior chemical shifts statistics, including 1HN, 15N, 13Cα, 13Cβ, 1Hα and carbonyl 13C nuclei, with corresponding structure coordinates.Dihedral angle information is usefu […]
Fine tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin type peptidyl prolyl isomerases
[…] setup but with S2 and distance restraint force constants set to zero. Correspondence of the ensembles to S2 parameters was checked with the CoNSEnsX server. Chemical shifts were back-calculated with shiftx2 with parameter settings corresponding to the experimental conditions for each molecule as described in the original publications (using default settings resulted in only minor changes not affe […]
Protein structure refinement using a quantum mechanics based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.
[…] rarchical agglomerative clustering.CheShift-2 () calculations were performed with the CheShift-2 PyMOL-plugin found at ; http://github.com/aloctavodia/cheshift. CamShift, PPM One, Sparta+, shAIC, and ShiftX2 () calculations are performed using the stand-alone predictors. Scripts to automate these predictions can be found at ; http://github.com/larsbratholm/cs_prediction.Much of the variation in so […]
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