Annotating Macromolecular Complexes in the Protein Data Bank:
Improving the FAIRness of Structure Data

J 2023

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

APPASAMY, Sri Devan, John BERRISFORD, Romana GÁBOROVÁ, Sreenath NAIR, Stephen ANYANGO et. al.

Základní údaje

Originální název

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

Autoři

APPASAMY, Sri Devan (garant), John BERRISFORD, Romana GÁBOROVÁ (703 Slovensko, domácí), Sreenath NAIR, Stephen ANYANGO, Sergei GRUDININ, Mandar DESHPANDE, David ARMSTRONG, Ivanna PIDRUCHNA, Joseph I. J. ELLAWAY, Grisell Díaz LEINES, Deepti GUPTA, Deborah HARRUS, Mihaly VARADI a Sameer VELANKAR

Vydání

Scientific Data, Nature Portfolio, 2023, 2052-4463

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.800 v roce 2022

Kód RIV

RIV/00216224:14740/23:00132419

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1038/s41597-023-02778-9

UT WoS

001116661600010

Klíčová slova anglicky

CRYSTAL-STRUCTURE; 20S PROTEASOME; MECHANISM; PDB; ASSEMBLIES; RECEPTOR; REVEALS; RESOURCE; YEAST; STATE

Štítky

CF BioData, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 4. 2024 09:14, Mgr. Eva Dubská

Anotace

V originále

Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB’s FAIR attributes, fostering more effective basic and translational research and scientific education.

Návaznosti

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

Citovat

APPASAMY, Sri Devan, John BERRISFORD, Romana GÁBOROVÁ, Sreenath NAIR, Stephen ANYANGO, Sergei GRUDININ, Mandar DESHPANDE, David ARMSTRONG, Ivanna PIDRUCHNA, Joseph I. J. ELLAWAY, Grisell Díaz LEINES, Deepti GUPTA, Deborah HARRUS, Mihaly VARADI a Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. Nature Portfolio, 2023, roč. 10, č. 1, s. 1-13. ISSN 2052-4463. Dostupné z: https://dx.doi.org/10.1038/s41597-023-02778-9.

@article{2346261,
   author = {Appasamy, Sri Devan and Berrisford, John and Gáborová, Romana and Nair, Sreenath and Anyango, Stephen and Grudinin, Sergei and Deshpande, Mandar and Armstrong, David and Pidruchna, Ivanna and Ellaway, Joseph I. J. and Leines, Grisell Díaz and Gupta, Deepti and Harrus, Deborah and Varadi, Mihaly and Velankar, Sameer},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41597-023-02778-9},
   keywords = {CRYSTAL-STRUCTURE; 20S PROTEASOME; MECHANISM; PDB; ASSEMBLIES; RECEPTOR; REVEALS; RESOURCE; YEAST; STATE},
   language = {eng},
   issn = {2052-4463},
   journal = {Scientific Data},
   title = {Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data},
   url = {https://doi.org/10.1038/s41597-023-02778-9},
   volume = {10},
   year = {2023}
}

TY  - JOUR
ID  - 2346261
AU  - Appasamy, Sri Devan - Berrisford, John - Gáborová, Romana - Nair, Sreenath - Anyango, Stephen - Grudinin, Sergei - Deshpande, Mandar - Armstrong, David - Pidruchna, Ivanna - Ellaway, Joseph I. J. - Leines, Grisell Díaz - Gupta, Deepti - Harrus, Deborah - Varadi, Mihaly - Velankar, Sameer
PY  - 2023
TI  - Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data
JF  - Scientific Data
VL  - 10
IS  - 1
SP  - 1-13
EP  - 1-13
PB  - Nature Portfolio
SN  - 20524463
KW  - CRYSTAL-STRUCTURE
KW  - 20S PROTEASOME
KW  - MECHANISM
KW  - PDB
KW  - ASSEMBLIES
KW  - RECEPTOR
KW  - REVEALS
KW  - RESOURCE
KW  - YEAST
KW  - STATE
UR  - https://doi.org/10.1038/s41597-023-02778-9
N2  - Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB’s FAIR attributes, fostering more effective basic and translational research and scientific education.
ER  -

APPASAMY, Sri Devan, John BERRISFORD, Romana GÁBOROVÁ, Sreenath NAIR, Stephen ANYANGO, Sergei GRUDININ, Mandar DESHPANDE, David ARMSTRONG, Ivanna PIDRUCHNA, Joseph I. J. ELLAWAY, Grisell Díaz LEINES, Deepti GUPTA, Deborah HARRUS, Mihaly VARADI a Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. \textit{Scientific Data}. Nature Portfolio, 2023, roč.~10, č.~1, s.~1-13. ISSN~2052-4463. Dostupné z: https://dx.doi.org/10.1038/s41597-023-02778-9.

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