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.
A method for the rapid and accurate prediction of NMR chemical shifts from protein structures. The calculations performed by CamShift are based on an approximate expression of the chemical shifts in terms of polynomial functions of interatomic distances. Since these functions are very fast to compute and readily differentiable, the CamShift approach can be utilized in standard protein structure calculation protocols.
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.
Detects referencing errors and to recalibrate the 1H and 13C chemical shift scales if needed. The analysis requires only that the signals be identified with distinct residue types (intra-residue spin systems). LACS allows errors in calibration to be detected and corrected in advance of sequence-specific assignments and secondary structure determinations. Signals that do not fit the linear model (outliers) deserve scrutiny since they could represent errors in identifying signals with a particular residue, or interesting features such as a cis-peptide bond. LACS provides the basis for the automated detection of such features and for testing reassignment hypotheses. Early detection and correction of errors in referencing and spin system identifications can improve the speed and accuracy of chemical shift assignments and secondary structure determinations. The input format is NMRSTAR 2.1 (BMRB) format, and. the result will be returned via email in a couple of minutes.
A database system for empirical prediction of backbone chemical shifts (N, HN, HA, CA, CB, CO) using a combination of backbone phi, psi torsion angles and sidechain chi1 angles from a given protein with known PDB coordinates.
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).