PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins

Tamas Lazar; Elizabeth Martínez-Pérez; Federica Quaglia; András Hatos; Lucía B. Chemes; Javier A. Iserte; Nicolás A. Méndez; Nicolás A. Garrone; Tadeo E. Saldaño; Julia Marchetti; Ana Julia Velez Rueda; Pau Bernadó; Martin Blackledge; Tiago N. Cordeiro; Eric Fagerberg; Julie D. Forman-Kay; Maria S. Fornasari; Toby J. Gibson; Gregory Neal W. Gomes; Claudiu C. Gradinaru; Teresa Head-Gordon; Malene Ringkjøbing Jensen; Edward A. Lemke; Sonia Longhi; Cristina Marino-Buslje; Giovanni Minervini; Tanja Mittag; Alexander Miguel Monzon; Rohit V. Pappu; Gustavo Parisi; Sylvie Ricard-Blum; Kiersten M. Ruff; Edoardo Salladini; Marie Skepö; Dmitri Svergun; Sylvain D. Vallet; Mihaly Varadi; Peter Tompa; Silvio C.E. Tosatto; Damiano Piovesan

doi:10.1093/nar/gkaa1021

PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins

Tamas Lazar, Elizabeth Martínez-Pérez, Federica Quaglia, András Hatos, Lucía B. Chemes, Javier A. Iserte, Nicolás A. Méndez, Nicolás A. Garrone, Tadeo E. Saldaño, Julia Marchetti, Ana Julia Velez Rueda, Pau Bernadó, Martin Blackledge, Tiago N. Cordeiro, Eric Fagerberg, Julie D. Forman-Kay, Maria S. Fornasari, Toby J. Gibson, Gregory Neal W. Gomes, Claudiu C. GradinaruTeresa Head-Gordon, Malene Ringkjøbing Jensen, Edward A. Lemke, Sonia Longhi, Cristina Marino-Buslje, Giovanni Minervini, Tanja Mittag, Alexander Miguel Monzon, Rohit V. Pappu, Gustavo Parisi, Sylvie Ricard-Blum, Kiersten M. Ruff, Edoardo Salladini, Marie Skepö, Dmitri Svergun, Sylvain D. Vallet, Mihaly Varadi, Peter Tompa, Silvio C.E. Tosatto, Damiano Piovesan

Forskningsoutput: Tidskriftsbidrag › Artikel i vetenskaplig tidskrift › Peer review

Sammanfattning

The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

Originalspråk	engelska
Sidor (från-till)	D404-D411
Antal sidor	8
Tidskrift	Nucleic Acids Research
Volym	49
Nummer	D1
DOI	https://doi.org/10.1093/nar/gkaa1021
Status	Published - 2021 jan. 8

Bibliografisk information

Funding Information:
PED is maintained as a service of the ELIXIR IDP community (URL: elixir-europe.org/communities/intrinsicallydisordered-proteins). This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 778247. Italian Ministry of University and Research (MIUR) to SCET [2017483NH8]; European Union's Horizon 2020 to SCET [778247]; Hungarian Scientific Research Fund (OTKA) to PT [K124670, K131702]; Universidad Nacional de Quilmes to GP [PUNQ 1309/19]; National Agency for the Promotion of Science and Technology (ANPCyT) to GP [PICT-2014-3430] and to LBC [PICT-2017-1924]; Fondation pour la Recherche M?dicale to SRB and SDV [DBI20141231336]; Natural Sciences and Engineering Research Council of Canada to CCG [RGPIN 2017-06030]; Agence Nationale de la Recherche (ANR) to PB [ANR-10-LABX-12-01]; National Institutes of Health (NIH) to JFK and THG [5R01GM127627-03]; German Ministry of Science and Education (SAS-BSOFT) to DS [16QK10A]; EU Horizon 2020 programme (iNEXT-Discovery) to DS [871037]; Vrije Universiteit Brussel (VUB) to PT [SRP51]; EM-P, NG, NM, JM are PhD students, AJVR, TES are Postdocs and GP, CM-B, JI, LBC and MSF are researchers of the National Research Council (CONICET) of Argentina. Funding for open access charge: Vrije Universiteit Brussel (VUB) [SRP51].

Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

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10.1093/nar/gkaa1021Licens: CC BY-NC

https://academic.oup.com/nar/article-abstract/49/D1/D404/6030232Licens: CC BY-NC

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Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Méndez, N. A., Garrone, N. A., Saldaño, T. E., Marchetti, J., Rueda, A. J. V., Bernadó, P., Blackledge, M., Cordeiro, T. N., Fagerberg, E., Forman-Kay, J. D., Fornasari, M. S., Gibson, T. J., Gomes, G. N. W., ... Piovesan, D. (2021). PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research, 49(D1), D404-D411. https://doi.org/10.1093/nar/gkaa1021

@article{0790a52fa49a4ce186894191f21881f2,

title = "PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins",

abstract = "The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.",

author = "Tamas Lazar and Elizabeth Mart{\'i}nez-P{\'e}rez and Federica Quaglia and Andr{\'a}s Hatos and Chemes, {Luc{\'i}a B.} and Iserte, {Javier A.} and M{\'e}ndez, {Nicol{\'a}s A.} and Garrone, {Nicol{\'a}s A.} and Salda{\~n}o, {Tadeo E.} and Julia Marchetti and Rueda, {Ana Julia Velez} and Pau Bernad{\'o} and Martin Blackledge and Cordeiro, {Tiago N.} and Eric Fagerberg and Forman-Kay, {Julie D.} and Fornasari, {Maria S.} and Gibson, {Toby J.} and Gomes, {Gregory Neal W.} and Gradinaru, {Claudiu C.} and Teresa Head-Gordon and Jensen, {Malene Ringkj{\o}bing} and Lemke, {Edward A.} and Sonia Longhi and Cristina Marino-Buslje and Giovanni Minervini and Tanja Mittag and Monzon, {Alexander Miguel} and Pappu, {Rohit V.} and Gustavo Parisi and Sylvie Ricard-Blum and Ruff, {Kiersten M.} and Edoardo Salladini and Marie Skep{\"o} and Dmitri Svergun and Vallet, {Sylvain D.} and Mihaly Varadi and Peter Tompa and Tosatto, {Silvio C.E.} and Damiano Piovesan",

note = "Funding Information: PED is maintained as a service of the ELIXIR IDP community (URL: elixir-europe.org/communities/intrinsicallydisordered-proteins). This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 778247. Italian Ministry of University and Research (MIUR) to SCET [2017483NH8]; European Union's Horizon 2020 to SCET [778247]; Hungarian Scientific Research Fund (OTKA) to PT [K124670, K131702]; Universidad Nacional de Quilmes to GP [PUNQ 1309/19]; National Agency for the Promotion of Science and Technology (ANPCyT) to GP [PICT-2014-3430] and to LBC [PICT-2017-1924]; Fondation pour la Recherche M?dicale to SRB and SDV [DBI20141231336]; Natural Sciences and Engineering Research Council of Canada to CCG [RGPIN 2017-06030]; Agence Nationale de la Recherche (ANR) to PB [ANR-10-LABX-12-01]; National Institutes of Health (NIH) to JFK and THG [5R01GM127627-03]; German Ministry of Science and Education (SAS-BSOFT) to DS [16QK10A]; EU Horizon 2020 programme (iNEXT-Discovery) to DS [871037]; Vrije Universiteit Brussel (VUB) to PT [SRP51]; EM-P, NG, NM, JM are PhD students, AJVR, TES are Postdocs and GP, CM-B, JI, LBC and MSF are researchers of the National Research Council (CONICET) of Argentina. Funding for open access charge: Vrije Universiteit Brussel (VUB) [SRP51]. Publisher Copyright: {\textcopyright} The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.",

year = "2021",

month = jan,

day = "8",

doi = "10.1093/nar/gkaa1021",

language = "English",

volume = "49",

pages = "D404--D411",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Lazar, T, Martínez-Pérez, E, Quaglia, F, Hatos, A, Chemes, LB, Iserte, JA, Méndez, NA, Garrone, NA, Saldaño, TE, Marchetti, J, Rueda, AJV, Bernadó, P, Blackledge, M, Cordeiro, TN, Fagerberg, E, Forman-Kay, JD, Fornasari, MS, Gibson, TJ, Gomes, GNW, Gradinaru, CC, Head-Gordon, T, Jensen, MR, Lemke, EA, Longhi, S, Marino-Buslje, C, Minervini, G, Mittag, T, Monzon, AM, Pappu, RV, Parisi, G, Ricard-Blum, S, Ruff, KM, Salladini, E, Skepö, M, Svergun, D, Vallet, SD, Varadi, M, Tompa, P, Tosatto, SCE & Piovesan, D 2021, 'PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins', Nucleic Acids Research, vol. 49, nr. D1, s. D404-D411. https://doi.org/10.1093/nar/gkaa1021

TY - JOUR

T1 - PED in 2021

T2 - A major update of the protein ensemble database for intrinsically disordered proteins

AU - Lazar, Tamas

AU - Martínez-Pérez, Elizabeth

AU - Quaglia, Federica

AU - Hatos, András

AU - Chemes, Lucía B.

AU - Iserte, Javier A.

AU - Méndez, Nicolás A.

AU - Garrone, Nicolás A.

AU - Saldaño, Tadeo E.

AU - Marchetti, Julia

AU - Rueda, Ana Julia Velez

AU - Bernadó, Pau

AU - Blackledge, Martin

AU - Cordeiro, Tiago N.

AU - Fagerberg, Eric

AU - Forman-Kay, Julie D.

AU - Fornasari, Maria S.

AU - Gibson, Toby J.

AU - Gomes, Gregory Neal W.

AU - Gradinaru, Claudiu C.

AU - Head-Gordon, Teresa

AU - Jensen, Malene Ringkjøbing

AU - Lemke, Edward A.

AU - Longhi, Sonia

AU - Marino-Buslje, Cristina

AU - Minervini, Giovanni

AU - Mittag, Tanja

AU - Monzon, Alexander Miguel

AU - Pappu, Rohit V.

AU - Parisi, Gustavo

AU - Ricard-Blum, Sylvie

AU - Ruff, Kiersten M.

AU - Salladini, Edoardo

AU - Skepö, Marie

AU - Svergun, Dmitri

AU - Vallet, Sylvain D.

AU - Varadi, Mihaly

AU - Tompa, Peter

AU - Tosatto, Silvio C.E.

AU - Piovesan, Damiano

N1 - Funding Information: PED is maintained as a service of the ELIXIR IDP community (URL: elixir-europe.org/communities/intrinsicallydisordered-proteins). This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 778247. Italian Ministry of University and Research (MIUR) to SCET [2017483NH8]; European Union's Horizon 2020 to SCET [778247]; Hungarian Scientific Research Fund (OTKA) to PT [K124670, K131702]; Universidad Nacional de Quilmes to GP [PUNQ 1309/19]; National Agency for the Promotion of Science and Technology (ANPCyT) to GP [PICT-2014-3430] and to LBC [PICT-2017-1924]; Fondation pour la Recherche M?dicale to SRB and SDV [DBI20141231336]; Natural Sciences and Engineering Research Council of Canada to CCG [RGPIN 2017-06030]; Agence Nationale de la Recherche (ANR) to PB [ANR-10-LABX-12-01]; National Institutes of Health (NIH) to JFK and THG [5R01GM127627-03]; German Ministry of Science and Education (SAS-BSOFT) to DS [16QK10A]; EU Horizon 2020 programme (iNEXT-Discovery) to DS [871037]; Vrije Universiteit Brussel (VUB) to PT [SRP51]; EM-P, NG, NM, JM are PhD students, AJVR, TES are Postdocs and GP, CM-B, JI, LBC and MSF are researchers of the National Research Council (CONICET) of Argentina. Funding for open access charge: Vrije Universiteit Brussel (VUB) [SRP51]. Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

PY - 2021/1/8

Y1 - 2021/1/8

N2 - The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

AB - The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

U2 - 10.1093/nar/gkaa1021

DO - 10.1093/nar/gkaa1021

M3 - Article

C2 - 33305318

AN - SCOPUS:85095859724

SN - 0305-1048

VL - 49

SP - D404-D411

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins

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