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

Journal Article · Thu May 06 00:00:00 EDT 2021 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkab314· OSTI ID:1781999

Sehnal, David ^[1]; Bittrich, Sebastian ^[2]; Deshpande, Mandar ^[3]; Svobodová, Radka ^[4]; Berka, Karel ^[5]; Bazgier, Václav ^[5]; Velankar, Sameer ^[3]; Burley, Stephen K. ^[6]; Koča, Jaroslav ^[4]; Rose, Alexander S. ^[2]

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1. CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic, Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
2. Research Collaboratory for Structural Bioinformatics (RCSB), San Diego Supercomputer Center, University of California San Diego, San Diego, CA 92093-0743, USA
3. Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
4. CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
5. Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc 771 46, Czech Republic
6. Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB); Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; Piscataway;  NJ 08854-8076; USA; Rutgers Cancer Institute of New Jersey; Rutgers; The State University of New Jersey; New Brunswick; NJ 08903-2681; USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB); San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; San Diego; CA 92093-0654; USA

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/.

• Sponsoring Organization: USDOE
• OSTI ID: 1781999
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: W1 Vol. 49; ISSN 0305-1048
• Publisher: Oxford University Press
• Country of Publication: United Kingdom
• Language: English