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Updated: Oct 1, 2025

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

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Published on: March 22, 2013

iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode.

Jiyao Wang¹, Philippe Youkharibache², Aron Marchler-Bauer¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.

Frontiers in Molecular Biosciences

|March 7, 2022

Summary

This summary is machine-generated.

iCn3D, a 3D molecular viewer, now supports large-scale structural data analysis using Python and Node.js scripts. This enables advanced ensemble analyses for growing databases like AlphaFold and improved structural biology research.

Keywords:

3d viewer Node.js script Python script batch mode delphi iCn3D structural analysis web-based

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Area of Science:

Structural Biology
Bioinformatics
Computational Chemistry

Background:

iCn3D evolved from a 3D molecular viewer to an interactive structural analysis tool.
It facilitates collaborative research through shareable, FAIR data-encapsulating URLs.
The increasing size of structural databases necessitates systematic analysis of large datasets.

Purpose of the Study:

To adapt iCn3D for systematic analysis of large structural datasets.
To enable scalable, batch-mode analysis of protein complexes and structural ensembles.
To introduce new features for enhanced molecular structure investigation.

Main Methods:

Conversion of iCn3D functionalities into Python and Node.js scripts.
Development of Python scripts for data export (e.g., secondary structures, images).
Implementation of Node.js scripts for batch processing and ensemble analysis.

Main Results:

iCn3D now supports large-scale structural data analysis via scripting.
Ensemble analyses are enabled for databases like AlphaFold and EM data.
New features include electrostatic potential, mutation visualization, and multiple structure alignment.

Conclusions:

iCn3D's scripting capabilities significantly enhance its utility for structural biology.
The software is now better equipped for analyzing large and growing structural datasets.
Advanced interactive features and scripting support facilitate comprehensive molecular analysis.