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Nucleic Acids Res. 2014 Jan;42(Database issue):D326-35. doi: 10.1093/nar/gkt960. Epub 2013 Oct 29.

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

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  • 1VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany, CEA, CNRS, UJF-Grenoble 1, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France, Indiana University School of Medicine; Indianapolis, IN, USA, Department of Chemistry, Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino, Italy, Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA, Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, Department of Chemistry, University of Cambridge, Cambridge, UK, Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest.

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.

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