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.

Basic information

Original name

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

Authors

APPASAMY, Sri Devan (guarantor), John BERRISFORD, Romana GÁBOROVÁ (703 Slovakia, belonging to the institution), 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 and Sameer VELANKAR

Edition

Scientific Data, Nature Portfolio, 2023, 2052-4463

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.800 in 2022

RIV identification code

RIV/00216224:14740/23:00132419

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

001116661600010

Keywords in English

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

Abstract

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.

Links

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological 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 and Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. Nature Portfolio, 2023, vol. 10, No 1, p. 1-13. ISSN 2052-4463. Available from: 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 and Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. \textit{Scientific Data}. Nature Portfolio, 2023, vol.~10, No~1, p.~1-13. ISSN~2052-4463. Available from: https://dx.doi.org/10.1038/s41597-023-02778-9.

Detailed Information on Publication Record