PALES is a versatile software for analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically or electrostatically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape and charge.
Nature Protocols, Epub: 27 March, (2008) 679-690
MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar couplings can be used to enhance assignment.
Compared to other currently available programs MARS is applicable to proteins above 15 kDa using only Ca and Cb chemical shift information with connectivity thresholds as high as 0.5 ppm and it is applicable to proteins with very high degeneracy such as partially or fully unfolded proteins. It offers improved assignment scores for proteins where data are missing for a substantial portion of residues and it has a good tolerance against erroneous chemical shifts. MARS assignment results can be directly read into the program SPARKY. This allows visual validation of the assignment results. Thus, several cycles of automatic assignment using MARS and manual validation on the screen can be performed, in order to complete assignment even in difficult cases.
J. Biomol. NMR, 30, (2004), 11-23.
J. Biomol. NMR, 30, (2004), 25-35.
HYdrodynamic CoUpling of Domains (HYCUD) is a Python-based program for prediction of rotational correlation time of folded protein domains in the context of flexible multidomain proteins and protein complexes with long disordered tails and/or interdomain linkers as well as intrinsically disordered proteins. HYCUD starts from a structural ensemble of the protein of interest together with a definition of its modular architecture, calculates the effective viscosity experienced locally by each of its modules and correspondingly scales the reorientational correlation time of isolated domains obtained through experiment or standard hydrodynamic calculations, and finally averages the scaled correlation times over the structural ensemble. The use of HYCUD has been validated in several protein systems differing in size, domain architecture, assembly state and disorder level.
Angew. Chem. Int. Ed.; 2013; Vol. 52(43), p11410-11414.
J. Am. Chem. Soc.; 2014; DOI: 10.1021/ja506820r.