pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

• Published in: Nucleic acids research Vol. 42; no. Database issue; pp. D326 - D335
• Main Authors: Varadi, Mihaly, Kosol, Simone, Lebrun, Pierre, Valentini, Erica, Blackledge, Martin, Dunker, A Keith, Felli, Isabella C, Forman-Kay, Julie D, Kriwacki, Richard W, Pierattelli, Roberta, Sussman, Joel, Svergun, Dmitri I, Uversky, Vladimir N, Vendruscolo, Michele, Wishart, David, Wright, Peter E, Tompa, Peter
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2014
• Subjects: Biochemistry, Molecular Biology; Databases, Protein; II. Protein sequence and structure, motifs and domains; Internet; Intrinsically Disordered Proteins; Intrinsically Disordered Proteins - chemistry; Life Sciences; Nuclear Magnetic Resonance, Biomolecular; Protein Unfolding; Scattering, Small Angle; Structural Biology; X-Ray Diffraction
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkt960

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.