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.
Allows prediction of nuclear shielding constants for a polypeptide sequence. ncIDP is a web application consisting of 3 reversible steps. The software can be interfaced with available protein chemical shift analysis tools, such as chemical shift index (CSI), structural propensity score assessment for intrinsically disordered proteins, and protein structure modeling from chemical shift information (CS-Rosetta).
Allows protein structure validation based on a quantum mechanics database of 13Cα chemical shifts. CheShift is a physics-based validation tool that permits users to determine the existence of local flaws in protein models. The software displays the differences between observed and predicted 13Cα chemical shifts by using a four-color code mapped onto a 3D protein model. A standalone version consisting of a PyMOL plugin is also available.
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.