title: The Protein Ensemble Database.
abstract: The scientific community's major conceptual notion of structural biology has recently shifted in emphasis from the classical structure-function paradigm due to the emergence of intrinsically disordered proteins (IDPs). As opposed to their folded cousins, these proteins are defined by the lack of a stable 3D fold and a high degree of inherent structural heterogeneity that is closely tied to their function. Due to their flexible nature, solution techniques such as small-angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) spectroscopy and fluorescence resonance energy transfer (FRET) are particularly well-suited for characterizing their biophysical properties. Computationally derived structural ensembles based on such experimental measurements provide models of the conformational sampling displayed by these proteins, and they may offer valuable insights into the functional consequences of inherent flexibility. The Protein Ensemble Database (http://pedb.vib.be) is the first openly accessible, manually curated online resource storing the ensemble models, protocols used during the calculation procedure, and underlying primary experimental data derived from SAXS and/or NMR measurements. By making this previously inaccessible data freely available to researchers, this novel resource is expected to promote the development of more advanced modelling methodologies, facilitate the design of standardized calculation protocols, and consequently lead to a better understanding of how function arises from the disordered state.
authors.affiliation: Department of Structural Biology, Vlaams Institute voor Biotechnologie (VIB), Brussels, Belgium.|Vrije Universiteit Brussel (VUB), Structural Biology Brussel (SBB), Brussels, Belgium.
authors.forename: Mihaly
authors.initials: M
authors.lastname: Varadi
authors.affiliation: Department of Structural Biology, Vlaams Institute voor Biotechnologie (VIB), Brussels, Belgium. ptompa@vub.ac.be.|Vrije Universiteit Brussel (VUB), Structural Biology Brussel (SBB), Brussels, Belgium. ptompa@vub.ac.be.|Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. ptompa@vub.ac.be.
authors.forename: Peter
authors.initials: P
authors.lastname: Tompa
mesh_terms: D030562:Databases, Protein; D016247:Information Storage and Retrieval; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry*; D053838:Scattering, Small Angle; D014584:User-Computer Interface; D014961:X-Ray Diffraction
chemical_list: D011506:Proteins
keywords: Calculation protocols; Database; Ensembles of structures; Experimental validation