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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F23%3A00132419" target="_blank" >RIV/00216224:14740/23:00132419 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1038/s41597-023-02778-9" target="_blank" >https://doi.org/10.1038/s41597-023-02778-9</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s41597-023-02778-9" target="_blank" >10.1038/s41597-023-02778-9</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/LM2018131" target="_blank" >LM2018131: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Scientific Data

ISSN

2052-4463

e-ISSN

2052-4463

Svazek periodika

10

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

13

Strana od-do

1-13

Kód UT WoS článku

001116661600010

EID výsledku v databázi Scopus

2-s2.0-85178178988