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

被引：86

作者：

Lazar, Tamas ^{[1
,2
]}

Martinez-Perez, Elizabeth ^{[3
,4
]}

Quaglia, Federica ^{[5
]}

Hatos, Andras ^{[5
]}

Chemes, Lucia B. ^{[6
]}

Iserte, Javier A. ^{[3
]}

Mendez, Nicolas A. ^{[6
]}

Garrone, Nicolas A. ^{[6
]}

Saldano, Tadeo E. ^{[7
]}

Marchetti, Julia ^{[7
]}

Velez Rueda, Ana Julia ^{[7
]}

Bernado, Pau ^{[8
]}

Blackledge, Martin ^{[9
]}

Cordeiro, Tiago N. ^{[8
,10
]}

Fagerberg, Eric ^{[11
]}

Forman-Kay, Julie D. ^{[12
,13
]}

Fornasari, Maria S. ^{[7
]}

Gibson, Toby J. ^{[4
]}

Gomes, Gregory-Neal W. ^{[14
,15
]}

Gradinaru, Claudiu C. ^{[14
,15
]}

Head-Gordon, Teresa ^{[16
,17
,18
]}

Jensen, Malene Ringkjobing ^{[9
]}

Lemke, Edward A. ^{[19
,20
]}

Longhi, Sonia ^{[21
]}

Marino-Buslje, Cristina ^{[3
]}

Minervini, Giovanni ^{[5
]}

Mittag, Tanja ^{[22
]}

Monzon, Alexander Miguel ^{[5
]}

Pappu, Rohit, V ^{[23
]}

Parisi, Gustavo ^{[7
]}

Ricard-Blum, Sylvie ^{[24
]}

Ruff, Kiersten M. ^{[23
]}

Salladini, Edoardo ^{[21
]}

Skepo, Marie ^{[11
,25
]}

Svergun, Dmitri ^{[26
]}

Vallet, Sylvain D. ^{[24
]}

Varadi, Mihaly ^{[27
]}

Tompa, Peter ^{[1
,2
,28
]}

Tosatto, Silvio C. E. ^{[5
]}

Piovesan, Damiano ^{[5
]}

机构：

[1] VIB VUB Ctr Struct Biol, Flanders Inst Biotechnol, B-1050 Brussels, Belgium

[2] Vrije Univ Brussel, Bioengn Sci Dept, Struct Biol Brussels, B-1050 Brussels, Belgium

[3] Fdn Inst Leloir, Bioinformat Unit, C1405BWE, Buenos Aires, DF, Argentina

[4] European Mol Biol Lab, Struct & Computat Biol Unit, D-69117 Heidelberg, Germany

[5] Univ Padua, Dept Biomed Sci, I-35131 Padua, Italy

[6] Univ Nacl San Martin, Inst Invest Biotecnol Dr Rodolfo A Ugalde, IIB UNSAM, IIBIO CONICET, RA-1650 Buenos Aires, DF, Argentina

[7] Univ Nacl Quilmes, Dept Ciencia & Tecnol, Lab Quim & Biol Computac, Bernal B1876BXD, Buenos Aires, DF, Argentina

[8] Univ Montpellier, Ctr Biochim Struct CBS, INSERM, CNRS, F-34090 Montpellier, France

[9] Univ Grenoble Alpes, IBS, CEA, CNRS, F-38000 Grenoble, France

[10] Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, Av Republ, P-2780157 Oeiras, Portugal

[11] Lund Univ, Theoret Chem, POB 124, SE-22100 Lund, Sweden

[12] Hosp Sick Children, Mol Med Program, Toronto, ON M5G 1X8, Canada

[13] Univ Toronto, Dept Biochem, Toronto, ON M5S 1A8, Canada

[14] Univ Toronto, Dept Phys, Toronto, ON M5S 1A7, Canada

[15] Univ Toronto Mississauga, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada

[16] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA

[17] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[18] Univ Calif Berkeley, Dept Chem & Biomol Engn, Berkeley, CA 94720 USA

[19] Johannes Gutenberg Univ Mainz, Bioctr, D-55128 Mainz, Germany

[20] Inst Mol Biol, D-55128 Mainz, Germany

[21] Aix Marseille Univ, Architecture & Fonct Macromol Biol AFMB, CNRS, F-13288 Marseille, France

[22] St Jude Childrens Res Hosp, Dept Struct Biol, Memphis, TN 38105 USA

[23] Washington Univ, Dept Biomed Engn, Ctr Sci & Engn Living Syst CSELS, St Louis, MO 63130 USA

[24] Univ Claude Bernard Lyon 1, Univ Lyon, CNRS,UMR 5246, INSA Lyon,CPE,Inst Mol & Supramol Chem & Biochem, F-69629 Lyon 07, France

[25] LINXS Lund Inst Adv Neutron & Xray Sci, S-22370 Lund, Sweden

[26] European Mol Biol Lab, Hamburg Unit, D-22607 Hamburg, Germany

[27] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Hinxton CB10 1SD, England

[28] Res Ctr Nat Sci, Inst Enzymol, H-1117 Budapest, Hungary

来源：

NUCLEIC ACIDS RESEARCH | 2021年 / 49卷 / D1期

基金：

匈牙利科学研究基金会; 美国国家卫生研究院; 加拿大自然科学与工程研究理事会;

关键词：

X-RAY-SCATTERING; STRUCTURAL-CHARACTERIZATION; NMR; ANNOTATIONS;

D O I：

10.1093/nar/gkaa1021

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 SAS-BDB. 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.

引用

页码：D404 / D411

页数：8

共 50 条

[41] Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning
Xu, Shijie
Onoda, Akira
Journal of Chemical Information and Modeling, 2024, 64 (07) : 2901 - 2911
[42] Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning
Xu, Shijie
Onoda, Akira
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2023, 64 (07) : 2901 - 2911
[43] Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins
Strodel, Birgit
JOURNAL OF MOLECULAR BIOLOGY, 2021, 433 (20)
[44] The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins
Meszaros, Balint
Simon, Istvan
Dosztanyi, Zsuzsanna
PHYSICAL BIOLOGY, 2011, 8 (03)
[45] Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation
Shrestha, Utsab R.
Juneja, Puneet
Zhang, Qiu
Gurumoorthy, Viswanathan
Borreguero, Jose M.
Urban, Volker
Cheng, Xiaolin
Pingali, Sai Venkatesh
Smith, Jeremy C.
O'Neill, Hugh M.
Petridis, Loukas
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (41) : 20446 - 20452
[46] SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy
Hermann, Markus R.
Hub, Jochen S.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (09) : 5103 - 5115
[47] Quantification of Compactness and Local Order in the Ensemble of the Intrinsically Disordered Protein FCP1
Gibbs, Eric B.
Showalter, Scott A.
JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 120 (34): : 8960 - 8969
[48] Characterizing Structural Ensembles of Intrinsically Disordered Proteins Determined via a Broad Ensemble Generator with Reweighting
Kashtanov, Stepan
Ytreberg, F. Marty
BIOPHYSICAL JOURNAL, 2012, 102 (03) : 631A - 631A
[49] Hyperphosphorylation of Intrinsically Disordered Tau Protein Induces an Amyloidogenic Shift in Its Conformational Ensemble
Zhu, Shaolong
Shala, Agnesa
Bezginov, Alexandr
Sljoka, Adnan
Audette, Gerald
Wilson, Derek J.
PLOS ONE, 2015, 10 (03):
[50] The prefoldin-like protein AtURI exhibits characteristics of intrinsically disordered proteins
Gomez-Minguez, Yaiza
Palacios-Abella, Alberto
Costigliolo-Rojas, Cecilia
Barber, Mariana
Hernandez-Villa, Laura
Urbez, Cristina
Alabadi, David
FEBS LETTERS, 2024, 598 (05) : 556 - 570

← 1 2 3 4 5 →