iCn3D: from Web-based 3D Viewer to Structure Analysis Tool in Batch Mode

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

iCn3D was originally released as a web-based 3D viewer, which allows users to create a custom view in a life-long, shortened URL to share with colleagues. Recently, iCn3D was converted to use JavaScript classes and could be used as a library to write Node.js scripts. Any interactive features in iCn3D can be converted to Node.js scripts to run in batch mode for a large data set. Currently the following Node.js script examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode: ligand-protein interaction, protein-protein interaction, change of interactions due to residue mutations, DelPhi electrostatic potential, and solvent accessible surface area. iCn3D PNG images can also be exported in batch mode using a Python script. Other recent features of iCn3D include the alignment of multiple chains from different structures, realignment, dynamic symmetry calculation for any subsets, 2D cartoons at different levels, and interactive contact maps. iCn3D can also be used in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.