Welcome to protein-nmr.org, the home of tools and software from the Mulder bioNMR lab

If you use our software programs or databases, then please cite our work. It is fair and polite, and it helps me maintain a lab to provide even more tools. For a more complete overview of our latest publications, please click here

POTENCI

You can predict your 'random coil chemical shifts' with POTENCI at the server here: https://st-protein02.chem.au.dk/potenci/

You can download POTENCI python source code for random coil chemical shift prediction at github: https://github.com/protein-nmr/POTENCI

 

CheZOD disorder database/predictor

You can download the CheZOD database used for testing disorder predictors at this link: http://www.protein-nmr.org/CheZOD.tar.gz

Predict your protein's CheZOD disorder score from assigned NMR chemical shifts at the server: https://st-protein.chem.au.dk/chezod

 

pepKalc

You can predict peptide/IDP titration curves (and compute pKa constants, etc.) at the server here: https://st-protein02.chem.au.dk/pepkalc/

 

ncIDP/ncSPC

You can predict your 'random coil chemical shifts' with ncIDP (2010) at the server here: https://st-protein02.chem.au.dk/ncIDP/

The ncSPC program for assessing structural propensities based on ncIDP is found here (for the moment): https://st-protein02.chem.au.dk/ncSPC/

 

Common Impurities Finder (for organic chemists, organometallic chemists, and biochemists)

Don't know what that peak is in your spectrum? Query it here against a database of common impurities based chemical shift and coupling pattern: common impurities

 

Bruker NMR Pulse sequence download (remove extension .txt when placing in PP directory)

3D HNCOCO - CO/N/H version (Yoshimura et al., JBNMR 2015): hncocogp3d1
3D HNCOCO - N/N/H version (Yoshimura et al., JBNMR 2015): hncocogp3d2
Arg head group CN experiment (Yoshimura et al., Angewandte Chemie 2017): arginine_head_group.yy
Paris-DECOR - fast backbone HX (Dass et al., ChemPhysChem 2019): hcacongp3d-hdx

 

The following papers describe the tools on this website. If you use them for your research, please cite them.

Sequence-specific random coil chemical shifts of intrinsically disordered proteins. (ncIDP)
Tamiola K, Acar B, Mulder FAA.
J Am Chem Soc. 2010 Dec 29;132(51):18000-3. doi: 10.1021/ja105656t

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. (ncSPC)
Tamiola
K, Mulder FAA.
Biochem Soc Trans. 2012 Oct;40(5):1014-20

There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order". (CheZOD database)
Nielsen JT, Mulder FAA
.
Front Mol Biosci. 2016 Feb 11;3:4. doi: 10.3389/fmolb.2016.00004

POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. (POTENCI)
Nielsen JT, Mulder FAA.
J Biomol NMR. 2018 Mar;70(3):141-165. doi: 10.1007/s10858-018-0166-5

Quality and bias of protein disorder predictors.
Nielsen JT, Mulder FAA.
Sci Rep. 2019 Mar 26;9(1):5137. doi: 10.1038/s41598-019-41644-w

Quantitative Protein Disorder Assessment using NMR Chemical Shifts (CheZOD predictor)
Nielsen JT, Mulder FAA.
Methods Mol Biol. 2019 (in press)

pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides. (pepKalc)
Tamiola K, Scheek RM, van der Meulen P, Mulder FAA.

Bioinformatics. 2018 Jun 15;34(12):2053-2060. doi: 10.1093/bioinformatics/bty033.