3rd Party Services

Here you can find links to services that might be useful in your work but are not managed by any West-Life partner. If you think there is an important service missing feel free to send us a note concerning which service should be added to the list.

NMR services

CoNSensX+

This server is specifically designed for the analysis of protein structural ensembles that are expected to reflect experimentally determined parameters as a whole. It also contains a simple greedy selection approach to select a (minimal) sub-ensemble corresponding to a selected set of parameters. The service is freely available at: http://consensx.itk.ppke.hu/

ncIDP random coil chemical shift calculator

This tool allows you to: calculate the random coil NMR chemical shifts for a protein Requires you to provide: amino acid sequence in one-letter notation (FASTA format) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. Tamiola K, Acar B, Mulder FA. J Am Chem Soc. 2010 Dec 29;132(51):18000-3. doi: 10.1021/ja105656t.

ncSPC secondary structure propensity calculator

This tool allows you to: calculate the propensity for secondary structure (alpha-helix or beta-sheet structure) Requires you to provide: assigned NMR chemical shifts (BMRB entry number or TALOS formatted file) Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. Tamiola K, Mulder FA. Biochem Soc Trans. 2012 Oct;40(5):1014-20.

ncIDP-assign Sparky plugin

This tool allows you to: add a plugin to the Sparky program for NMR resonance assignment to facilitate assignments for IDPs Requires you to provide: -- ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Tamiola K, Mulder FA. Bioinformatics. 2011 Apr 1;27(7):1039-40. doi: 10.1093/bioinformatics/btr054.

Common NMR impurities database and analysis tool

This tool allows you to: establish the identity of impurities in NMR spectra for biological NMR (database in D2O) and organic chemistry (several solvents) Requires you to provide: chemical shift position of signals and information about spin-spin coupling patterns

MX

Grade

Grade generates geometrical restraints for novel small molecules in protein complexes, for both ligand placement into density maps and subsequent refinement. These restraints can be used in autoBUSTER, rhofit, Refmac and Coot.

SAXS

pyDockSAXS

pyDockSAXS server is a web server for rigid-body protein-protein docking that combines computational and experimental information. On one side the server uses the new version of pyDock (pyDock 3.0) to energetically evaluate the interaction surface of multiple docking poses. On the other side, the server evaluates the capacity of each pose to describe the experimental curve of SAXS with the program CRYSOL. The appropriate combination of both scoring functions yields predictions of the 3D arrangement of the complex in solution.