Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract

Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Hydroxyurea—The Good, the Bad and the Ugly

“…( F ) Hydroxyurea inhibits PCET within RNR by proton-coupled electron transfer, most probably mediated by a hydrogen-bonded proton wire [ 35 ]. The images in ( A , B ) were generated using Mol*Viewer [ 46 ].…”

Association of Alpha-Crystallin with Fiber Cell Plasma Membrane of the Eye Lens Accompanied by Light Scattering and Cataract Formation

“…These functions of crystallins are significant for maintaining lens transparency and preventing cataract formation [27]. [20] created with Mol* [28]. (b) Pseudo-atomic model of recombinant human αB-crystallin 24-mer assembly.…”

“…(b) Pseudo-atomic model of recombinant human αB-crystallin 24-mer assembly. Image from the RCSB PDB (rcsb.org, accessed on: 8 April 2021) of PDB ID 3J07 [21] created with Mol* [28].…”

TMEM135 is a Novel Regulator of Mitochondrial Dynamics and Physiology with Implications for Human Health Conditions

“…Interestingly, the function of SMPD3 is to hydrolyze sphingomyelin to form ceramide and phosphocholine [ 93 , 94 , 95 ]. SMPD3 has a crystallized structure (5UVG) that has two calcium ion ligands [ 96 , 97 ]. Given the localization TMEM135 has with lipid droplets and the experimental evidence of interaction and shared homology with SMPD3, we postulate that TMEM135 has a role in altering Ca 2+ dynamics.…”