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Protein chemical shift detection software tools | NMR-based proteomics data analysis

NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model

Source text:
(Dehof et al., 2013) NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction. BMC Bioinformatics.

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VASCO / Validation of Archived chemical Shifts through atomic Coordinates
Uses the PDB (Protein Data Bank) and BMRB (Biological Magnetic Resonance Bank) archives and performs a statistical analysis, which takes into account the solvent accessibility of all heavy atoms, the secondary structure information and the reported chemical shift values. VASCO corrects and reports chemical shift referencing inconsistencies, identifies individual chemical shift outliers and provides a Z-score for each deviation from the expected mean value. The method can be extended to use other information (e.g., dihedral angles) by further subdividing the data and to other nuclei and/or molecule types (e.g., RNA and DNA), although this only becomes possible with increasing data archive size.
Provides automatic reference correction for CA, CB, C' and N chemical shifts. CheckShift is based on a comparison between the cumulative distribution function (cdf) of the target chemical shifts with the cumulative distribution function of a set of reference chemical shifts. The closer the two functions are, the higher is the confidence that the chemical shifts are referenced according to the IUPAC standard. CheckShift does not require additional data and is therefore applicable to data sets where structures are not available. Therefore, CheckShift provides the possibility to re-reference chemical shifts prior to their use as structural constraints.
Provides a means for rapid assignments and book-keeping of Nuclear Magnetic Resonance (NMR) titration spectra. NvMap is a NMRViewJ module capable of taking a reference peak list and then copying the peak numbers and assignments of this peak list to any number of given spectra. It includes menus for picking among the imported peak lists and datasets, and allows the user to name new peaklists. The user can also specify distance and peak picking thresholds as desired. This module greatly speeds up the data analysis process for any chemical shift perturbation analysis.
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