Biomolecular NMR

Purdue University

Latest sequences and programs downloadable from

Pulse sequences

hacacon_NH_ND_exchange sequence for accurately measuring amide solvent exchange rates. Chevelkov et al., to be published. Available on request from or

hsqc_HN35_T sequence for measuring relaxation dispersion profiles of amide protons in deuterated proteins. Eichmüller and Skrynnikov, J. Biomol. NMR. 2005, 32, 281-293. Available on request from

hacacon_NH_ND_T1, hacacon_NH_ND_T sequences are used for measuring nitrogen relaxation rates in 15N(-1H) and 15N(-2H). Xu et al., J. Am. Chem. Soc. 2005, 127, 3220-3229. Available on request from


RDCA (Conformist) program refines the relative domain orientation in multi-domain proteins based on residual dipolar couplings. (N. R. Skrynnikov et al., J. Mol Biol. 2000, 295, 1265-1273). Coded in Matlab (Mathworks Inc.) Also, XPLOR/CNS scripts for adjusting domain orientations (N. K. Goto, N. R. Skrynnikov et al., J. Mol Biol. 2001, 308, 745-764). Available on request from

Redfield/Liouville programs calculate analytical expressions for Redfield relaxation matrix and superhamiltonain matrix. Coded in Maple (Waterloo Software Inc.). Available on request from

PMAG module for CNS/XPLOR incorporates paramagnetic relaxation rate enhancements into protein structure refinement (L. W. Donaldson, N. R. Skrynnikov et al, J. Am. Chem. Soc. 2001, 123, 9843-9847). Available on request from

MD_Tools: a collection of scripts for manipulating MD trajectories (selecting groups of atoms, superimposing frames, etc.) and calculating structural and NMR-related parameters (dihedral angles, correlation functions, relaxation rates, etc.). Written in matlab, with several modules in python and C. Available upon request from and

PRE: a collection of scripts for calculating PRE rates in unfolded proteins, including analytical and numeric solutions, as well as MD simulation setup. (Y. Xue et al. Prot. Sci. 2009, in press). Written in matlab, python, C, and XPLOR macro language. Available upon request from, and

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