Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964940/
https://www.ncbi.nlm.nih.gov/pubmed/24174539
http://dx.doi.org/10.1093/nar/gkt960
_version_ 1782479262653087744
author 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
author_facet 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
author_sort Varadi, Mihaly
collection PubMed
description 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.
format Online
Article
Text
id pubmed-3964940
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-39649402014-03-25 pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins 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 Nucleic Acids Res II. Protein sequence and structure, motifs and domains 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. Oxford University Press 2014-01-01 2013-10-29 /pmc/articles/PMC3964940/ /pubmed/24174539 http://dx.doi.org/10.1093/nar/gkt960 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle II. Protein sequence and structure, motifs and domains
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
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title_full pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title_fullStr pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title_full_unstemmed pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title_short pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
title_sort pe-db: a database of structural ensembles of intrinsically disordered and of unfolded proteins
topic II. Protein sequence and structure, motifs and domains
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964940/
https://www.ncbi.nlm.nih.gov/pubmed/24174539
http://dx.doi.org/10.1093/nar/gkt960
work_keys_str_mv AT varadimihaly pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT kosolsimone pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT lebrunpierre pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT valentinierica pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT blackledgemartin pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT dunkerakeith pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT felliisabellac pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT formankayjulied pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT kriwackirichardw pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT pierattelliroberta pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT sussmanjoel pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT svergundmitrii pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT uverskyvladimirn pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT vendruscolomichele pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT wishartdavid pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT wrightpetere pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins
AT tompapeter pedbadatabaseofstructuralensemblesofintrinsicallydisorderedandofunfoldedproteins