PE-DB: A database of structural ensembles of intrinsically disordered and of unfolded proteins

Mihaly Varadi, Simone Kosol, Pierre Lebrun, Erica Valentini, Martin Blackledge, A. Keith Dunker, Isabella C. Felli, Julie D. Forman-Kay, Richard W. Kriwacki, Roberta Pierattelli, Joel Sussman, Dmitri I. Svergun, Vladimir N. Uversky, Michele Vendruscolo, David Wishart, Peter E. Wright, Peter Tompa

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Abstract

The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states.

Original languageEnglish (US)
Pages (from-to)D326-D335
JournalNucleic acids research
Volume42
Issue numberD1
DOIs
StatePublished - Jan 1 2014

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ASJC Scopus subject areas

  • Genetics

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Varadi, M., Kosol, S., Lebrun, P., Valentini, E., Blackledge, M., Dunker, A. K., Felli, I. C., Forman-Kay, J. D., Kriwacki, R. W., Pierattelli, R., Sussman, J., Svergun, D. I., Uversky, V. N., Vendruscolo, M., Wishart, D., Wright, P. E., & Tompa, P. (2014). PE-DB: A database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic acids research, 42(D1), D326-D335. https://doi.org/10.1093/nar/gkt960