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

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

doi:10.3389/fmolb.2022.831740

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

Front Mol Biosci. 2022 Feb 17:9:831740. doi: 10.3389/fmolb.2022.831740. eCollection 2022.

Authors

Jiyao Wang¹, Philippe Youkharibache², Aron Marchler-Bauer¹, Christopher Lanczycki¹, Dachuan Zhang¹, Shennan Lu¹, Thomas Madej^{1

2}, Gabriele H Marchler¹, Tiejun Cheng¹, Li Chuin Chong³, Sarah Zhao⁴, Kevin Yang⁵, Jack Lin⁶, Zhiyu Cheng⁷, Rachel Dunn⁸, Sridhar Acharya Malkaram⁹, Chin-Hsien Tai², David Enoma¹⁰, Ben Busby¹¹, Nicholas L Johnson¹², Francesco Tabaro¹³, Guangfeng Song¹, Yuchen Ge¹⁴

Affiliations

¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.
² National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
³ Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkey.
⁴ Cary Academy, Cary, NC, United States.
⁵ University of Maryland, College Park, MD, United States.
⁶ University of Washington, Tacoma, WA, United States.
⁷ University of California, Irvine, Irvine, CA, United States.
⁸ University of British Columbia, Vancouver, BC, Canada.
⁹ West Virginia State University, Institute, WV, United States.
¹⁰ Noma Technology, Port Harcourt, Nigeria.
¹¹ DNAnexus, Pittsburgh, PA, United States.
¹² National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.
¹³ European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
¹⁴ Johns Hopkins University, Baltimore, MD, United States.

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.

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