Biomolecular NMR

Latest sequences and programs downloadable from https://purcell.chem.purdue.edu/php/download/

Pulse sequences

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

hsqc_HN35_T_1ρ 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 nikolai@purdue.edu.

hacacon_NH_ND_T₁, hacacon_NH_ND_T_1ρ 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 nikolai@purdue.edu

Software

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 nikolai@purdue.edu

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

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 nikolai@purdue.edu

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 nikolai@purdue.edu and yixue@purdue.edu

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 nikolai@purdue.edu, yixue@purdue.edu and podkorytov@purdue.edu