ICn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode.

Jiyao Wang,Yuchen Ge,Gabriele H Marchler,Rachel Dunn,Guangfeng Song,Ben Busby,Philippe Youkharibache,Thomas Madej,Sridhar Acharya Malkaram,Zhiyu Cheng,Tiejun Cheng,Nicholas L Johnson,Kevin Yang,Dachuan Zhang,Sarah Zhao,David Enoma,Francesco Tabaro,Chong Li ,Jack J Lin ,Aron Marchler‐Bauer ,Chin‐Hsien Tai ,Christopher J Lanczycki ,Shuo Lu

doi:10.3389/fmolb.2022.831740

Abstract

iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node. js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node. js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node. js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electron Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.

Highlights

With the release of more and more AlphaFold (Jumper et al, 2021) or RoseTTAFold (Baek et al, 2021) predicted structures and experimentally determined structures, it is important to be able to do structural analysis in batch mode
The custom view can be reproduced with a permanent sharable link https://structure.ncbi
Users can use either Python scripts or Node. js scripts to a large set of 3D structures

Summary

Introduction

With the release of more and more AlphaFold (Jumper et al, 2021) or RoseTTAFold (Baek et al, 2021) predicted structures and experimentally determined structures, it is important to be able to do structural analysis in batch mode. Our recent development on iCn3D helps fill this need. ICn3D is a web-based 3D structure viewer, and an analysis tool either interactively or in batch mode. Js scripts, which call functions in iCn3D. All interactive structural analyses in iCn3D could be converted to analyses in batch mode using either Python scripts or Node. This feature has been available since we modernized the code of iCn3D to use JavaScript classes. All recent additions are colored in orange. “Users” could use iCn3D for 3D views, annotations, or structural analyses through three different “Front End” interfaces: web pages, Jupyter Notebook, or Python/Node. The backends are “RESTful APIs” to retrieve 3D coordinates, annotations, or analysis data

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