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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Online carbohydrate 3D structure validation with the Privateer web app.

Jordan S Dialpuri¹, Haroldas Bagdonas¹, Lucy C Schofield¹

¹York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom.

Acta Crystallographica. Section F, Structural Biology Communications

|January 24, 2024

Summary

A new web app for Privateer software simplifies the validation and analysis of 3D glycan structures. This tool enhances the structural biology pipeline by providing online access without installation, ensuring data privacy.

Keywords:

N-glycans N-glycosylation Privateer carbohydrates polysaccharides validation web apps

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Area of Science:

Structural Biology
Computational Chemistry
Biochemistry

Background:

Carbohydrate 3D structure validation is crucial for the Protein Data Bank deposition pipeline due to inherent complexities.
The Privateer software offers integrated methods for analyzing, refining, and visualizing glycan 3D atomic structures, including ligands and protein modifiers.

Purpose of the Study:

To present the Privateer web application, an accessible online version of the Privateer software.
To enable structural biologists to analyze carbohydrate ligands and protein glycosylation efficiently and securely via a web browser.

Main Methods:

Development of a web application interface for the existing Privateer software.
Ensuring the web app runs locally on the user's machine for data confidentiality.
Implementing a self-updating mechanism for the web application.

Main Results:

The Privateer web app is available online without requiring installation.
The tool allows for quick and simple analysis of carbohydrate ligands and protein glycosylation.
User data remains confidential as the analysis runs locally.

Conclusions:

The Privateer web app provides a user-friendly, accessible, and secure platform for glycan structure analysis.
This tool streamlines the structural biology workflow by removing installation barriers and ensuring data privacy.