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SAMPLEX: unbiased definition of active residues for HADDOCK

SAMPLEX: Smooth Automated Mapping of Proteins from Listed EXtreme

The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.

SAMPLEX is an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.

The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information. It requires as input a 3D structure of the protein, and a data table containing residue numbers with their associated property to be classified.

 

Version:

1.0 (August, 2009)

Authors:

Krzeminski, M., Loth, K., Boelens R. and A.M.J.J. Bonvin, Utrecht University

Contact:

Bijvoet Center for Biomolecular Research
Padualaan 8, 3584 CH Utrecht, the Netherlands
Email: a.m.j.j.bonvin_AT_uu.nl
Phone: +31-30-2533859
Fax: +31-30-2537623

 

SAMPLEX (a python script), together with example data can be freely downloaded here.

 

M. Krzeminski, K. Loth, R. Boelens and A.M.J.J. Bonvin
"SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes."
BMC Bioinformatics, 11, 51 (2010).

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And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

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European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

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