PDBe and PDBe-KB: Providing high-quality, up-to-date and
integrated resources of macromolecular structures to support
basic and applied research and education

J 2022

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education

VARADI, Mihaly; Stephen ANYANGO; Sri Devan APPASAMY; David ARMSTRONG; Marcus BAGE et. al.

Basic information

Original name

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education

Authors

VARADI, Mihaly; Stephen ANYANGO; Sri Devan APPASAMY; David ARMSTRONG; Marcus BAGE; John BERRISFORD; Preeti CHOUDHARY; Damian BERTONI; Mandar DESHPANDE; Grisell Diaz LEINES; Joseph ELLAWAY; Genevieve EVANS; Romana GÁBOROVÁ (703 Slovakia); Deepti GUPTA; Aleksandras GUTMANAS; Deborah HARRUS; Gerard J KLEYWEGT; Weslley Morellato BUENO; Nurul NADZIRIN; Sreenath NAIR; Lukas PRAVDA; Marcelo Querino Lima AFONSO; David SEHNAL (203 Czech Republic, belonging to the institution); Ahsan TANWEER; James TOLCHARD; Charlotte ABRAMS; Roisin DUNLOP and Sameer VELANKAR

Edition

Protein Science, Wiley, 2022, 0961-8368

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 8.000

RIV identification code

RIV/00216224:14310/22:00128597

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1002/pro.4439

UT WoS

000860758200001

EID Scopus

2-s2.0-85138849602

Keywords in English

bioinformatics; databases; protein data bank; structural biology

Abstract

In the original language

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; ) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; ), to the PDBe Knowledge Base (PDBe-KB; ), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.

Links

90131, large research infrastructures

Name: ELIXIR-CZ II

Cite

VARADI, Mihaly; Stephen ANYANGO; Sri Devan APPASAMY; David ARMSTRONG; Marcus BAGE; John BERRISFORD; Preeti CHOUDHARY; Damian BERTONI; Mandar DESHPANDE; Grisell Diaz LEINES; Joseph ELLAWAY; Genevieve EVANS; Romana GÁBOROVÁ; Deepti GUPTA; Aleksandras GUTMANAS; Deborah HARRUS; Gerard J KLEYWEGT; Weslley Morellato BUENO; Nurul NADZIRIN; Sreenath NAIR; Lukas PRAVDA; Marcelo Querino Lima AFONSO; David SEHNAL; Ahsan TANWEER; James TOLCHARD; Charlotte ABRAMS; Roisin DUNLOP and Sameer VELANKAR. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Science. Wiley, 2022, vol. 31, No 10, p. 1-10. ISSN 0961-8368. Available from: https://dx.doi.org/10.1002/pro.4439.

@article{2253740,
   author = {Varadi, Mihaly and Anyango, Stephen and Appasamy, Sri Devan and Armstrong, David and Bage, Marcus and Berrisford, John and Choudhary, Preeti and Bertoni, Damian and Deshpande, Mandar and Leines, Grisell Diaz and Ellaway, Joseph and Evans, Genevieve and Gáborová, Romana and Gupta, Deepti and Gutmanas, Aleksandras and Harrus, Deborah and Kleywegt, Gerard J and Bueno, Weslley Morellato and Nadzirin, Nurul and Nair, Sreenath and Pravda, Lukas and Afonso, Marcelo Querino Lima and Sehnal, David and Tanweer, Ahsan and Tolchard, James and Abrams, Charlotte and Dunlop, Roisin and Velankar, Sameer},
   article_number = {10},
   doi = {http://dx.doi.org/10.1002/pro.4439},
   keywords = {bioinformatics; databases; protein data bank; structural biology},
   language = {eng},
   issn = {0961-8368},
   journal = {Protein Science},
   title = {PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education},
   url = {https://onlinelibrary.wiley.com/doi/10.1002/pro.4439},
   volume = {31},
   year = {2022}
}

TY  - JOUR
ID  - 2253740
AU  - Varadi, Mihaly - Anyango, Stephen - Appasamy, Sri Devan - Armstrong, David - Bage, Marcus - Berrisford, John - Choudhary, Preeti - Bertoni, Damian - Deshpande, Mandar - Leines, Grisell Diaz - Ellaway, Joseph - Evans, Genevieve - Gáborová, Romana - Gupta, Deepti - Gutmanas, Aleksandras - Harrus, Deborah - Kleywegt, Gerard J - Bueno, Weslley Morellato - Nadzirin, Nurul - Nair, Sreenath - Pravda, Lukas - Afonso, Marcelo Querino Lima - Sehnal, David - Tanweer, Ahsan - Tolchard, James - Abrams, Charlotte - Dunlop, Roisin - Velankar, Sameer
PY  - 2022
TI  - PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education
JF  - Protein Science
VL  - 31
IS  - 10
SP  - 1-10
EP  - 1-10
PB  - Wiley
SN  - 09618368
KW  - bioinformatics
KW  - databases
KW  - protein data bank
KW  - structural biology
UR  - https://onlinelibrary.wiley.com/doi/10.1002/pro.4439
N2  - The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; ) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; ), to the PDBe Knowledge Base (PDBe-KB; ), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
ER  -

VARADI, Mihaly; Stephen ANYANGO; Sri Devan APPASAMY; David ARMSTRONG; Marcus BAGE; John BERRISFORD; Preeti CHOUDHARY; Damian BERTONI; Mandar DESHPANDE; Grisell Diaz LEINES; Joseph ELLAWAY; Genevieve EVANS; Romana GÁBOROVÁ; Deepti GUPTA; Aleksandras GUTMANAS; Deborah HARRUS; Gerard J KLEYWEGT; Weslley Morellato BUENO; Nurul NADZIRIN; Sreenath NAIR; Lukas PRAVDA; Marcelo Querino Lima AFONSO; David SEHNAL; Ahsan TANWEER; James TOLCHARD; Charlotte ABRAMS; Roisin DUNLOP and Sameer VELANKAR. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. \textit{Protein Science}. Wiley, 2022, vol.~31, No~10, p.~1-10. ISSN~0961-8368. Available from: https://dx.doi.org/10.1002/pro.4439.

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