Downloads

In the Downloads menu you will find our downloadable data and software.

The ncIDP-assign extension for Sparky is a self-contained compressed archive that you can install on your computer if you use Sparky. It will add a database of random coil chemical shifts and a tool for assisting the assignment of triple resonance spectra for intrinsically disordered proteins.

ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Tamiola K, Mulder FAA. Bioinformatics. 2011 Apr 1;27(7):1039-40

Pulse sequences refer to recent Bruker NMR pulse sequences for (i) The facile assignment of intrinsically disordered proteins by use of 3D HN(CO)NH spectroscopy (ii) The determination of Arg protonation states.

Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C’ chemical shifts of multiple contiguous residues in highly resolved 3D spectra. Yoshimura Y, Kulminskaya NV, Mulder FAA. J Biomol NMR. 2015 Feb;61(2):109-21

Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Yoshimura Y, Oktaviani NA, Yonezawa K, Kamikubo H, Mulder FAA. Angew Chem Int Ed Engl. 2017 Jan 2;56(1):239-242.

The CheZOD database contains NMR chemical shift data for a selection of ~120 proteins, which span the full gamut from full protein order to complete protein disorder. This database has been used to investigate the patterns of protein disorder. These are far from random!

There is Diversity in Disorder-“In all Chaos there is a Cosmos, in all Disorder a Secret Order”. Nielsen JT, Mulder FAA. Front Mol Biosci. 2016 Feb 11;3:4.

The link to POTENCI source code provides the python script for download – including a README file

POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. Nielsen JT, Mulder FAA. J. Biomol. NMR 2018 Feb 5; DOI: 10.1007/s10858-018-0166-5