Harnessing the 3D-Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data.
3D‐Beacons
FAIR data access
federated data network
macromolecular structures
programmatic access
structural bioinformatics
Journal
Current protocols
ISSN: 2691-1299
Titre abrégé: Curr Protoc
Pays: United States
ID NLM: 101773894
Informations de publication
Date de publication:
May 2024
May 2024
Historique:
medline:
9
5
2024
pubmed:
9
5
2024
entrez:
9
5
2024
Statut:
ppublish
Résumé
Recent advancements in protein structure determination and especially in protein structure prediction techniques have led to the availability of vast amounts of macromolecular structures. However, the accessibility and integration of these structures into scientific workflows are hindered by the lack of standardization among publicly available data resources. To address this issue, we introduced the 3D-Beacons Network, a unified platform that aims to establish a standardized framework for accessing and displaying protein structure data. In this article, we highlight the importance of standardized approaches for accessing protein structure data and showcase the capabilities of 3D-Beacons. We describe four protocols for finding and accessing macromolecular structures from various specialist data resources via 3D-Beacons. First, we describe three scenarios for programmatically accessing and retrieving data using the 3D-Beacons API. Next, we show how to perform sequence-based searches to find structures from model providers. Then, we demonstrate how to search for structures and fetch them directly into a workflow using JalView. Finally, we outline the process of facilitating access to data from providers interested in contributing their structures to the 3D-Beacons Network. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Programmatic access to the 3D-Beacons API Basic Protocol 2: Sequence-based search using the 3D-Beacons API Basic Protocol 3: Accessing macromolecules from 3D-Beacons with JalView Basic Protocol 4: Enhancing data accessibility through 3D-Beacons.
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1047Subventions
Organisme : Wellcome Trust
ID : 223739/Z/21/Z
Pays : United Kingdom
Informations de copyright
© 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.
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