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/.

CEITEC Central European Institute of Technology Masaryk University Brno 625 00 Czech Republic

Department of Physical Chemistry Faculty of Science Palacký University Olomouc Olomouc 771 46 Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno 602 00 Czech Republic

Protein Data Bank in Europe Wellcome Genome Campus Hinxton CB10 1SD UK

Research Collaboratory for Structural Bioinformatics Protein Data Bank Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey Piscataway NJ 08854 8076 USA

Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego San Diego CA 92093 0654 USA

Research Collaboratory for Structural Bioinformatics San Diego Supercomputer Center University of California San Diego San Diego CA 92093 0743 USA

Rutgers Cancer Institute of New Jersey Rutgers The State University of New Jersey New Brunswick NJ 08903 2681 USA

Zobrazit více v PubMed

Burley S.K., Kurisu G., Markley J.L., Nakamura H., Velankar S., Berman H.M., Sali A., Schwede T., Trewhella J.. PDB-Dev: a prototype system for depositing integrative/hybrid structural models. Structure. 2017; 25:1317–1318. PubMed PMC

Sali A., Berman H.M., Schwede T., Trewhella J., Kleywegt G., Burley S.K., Markley J., Nakamura H., Adams P., Bonvin A.M.J.J.et al. .. Outcome of the first wwPDB hybrid/integrative methods task force workshop. Structure. 2015; 23:1156–1167. PubMed PMC

Kummer E., Ban N.. Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1. EMBO J. 2020; 39:e104820. PubMed PMC

Chavent M., Duncan A.L., Rassam P., Birkholz O., Hélie J., Reddy T., Beliaev D., Hambly B., Piehler J., Kleanthous C.et al. .. How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins. Nat. Commun. 2018; 9:2846. PubMed PMC

Jung J., Nishima W., Daniels M., Bascom G., Kobayashi C., Adedoyin A., Wall M., Lappala A., Phillips D., Fischer W.et al. .. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. J. Comput. Chem. 2019; 40:1919–1930. PubMed PMC

Asbury T.M., Mitman M., Tang J., Zheng W.J.. Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinformatics. 2010; 11:444. PubMed PMC

Singharoy A., Maffeo C., Delgado-Magnero K.H., Swainsbury D.J.K., Sener M., Kleinekathöfer U., Vant J.W., Nguyen J., Hitchcock A., Isralewitz B.et al. .. Atoms to phenotypes: molecular design principles of cellular energy metabolism. Cell. 2019; 179:1098–1111. PubMed PMC

Sehnal D., Rose A.S., Koča J., Burley S.K., Velankar S.. Byška J., Krone M., Sommer B.. Mol*: Towards a common library and tools for web molecular graphics. Proceedings of the Workshop on Molecular Graphics and Visual Analysis of Molecular Data. 2018; 29–33.

Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E.. The Protein Data Bank. Nucleic Acids Res. 2000; 28:235–242. PubMed PMC

Mir S., Alhroub Y., Anyango S., Armstrong D.R., Berrisford J.M., Clark A.R., Conroy M.J., Dana J.M., Deshpande M., Gupta D.et al. .. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res. 2018; 46:D486–D492. PubMed PMC

Andreeva A., Kulesha E., Gough J., Murzin A.G.. The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. Nucleic Acids Res. 2020; 48:D376–D382. PubMed PMC

Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E.L.L., Tosatto S.C.E., Paladin L., Raj S., Richardson L.J.et al. .. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021; 49:D412–D419. PubMed PMC

The Uniprot Consortium UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021; 49:D480–D489. PubMed PMC

Sehnal D., Deshpande M., Svobodová Vařeková R., Mir S., Berka K., Midlik A., Pravda L., Velankar S., Koča J.. LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. Nat. Methods. 2017; 14:1121–1122. PubMed

Rose A.S., Hildebrand P.W.. NGL Viewer: a web application for molecular visualization. Nucleic Acids Res. 2015; 43:W576–W579. PubMed PMC

Rose A.S., Bradley A.R., Valasatava Y., Duarte J.M., Prlić A., Rose P.W.. Web-based molecular graphics for large complexes. Web3D ’16: Proceedings of the 21st International Conference on Web3D Technology. 2016; 185–186.

Sehnal D., Pravda L., Svobodová Vařeková R., Ionescu C.-M., Koča J.. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. 2015; 43:W383–W388. PubMed PMC

Bradley A.R., Rose A.S., Pavelka A., Valasatava Y., Duarte J.M., Prlić A., Rose P.W.. MMTF—an efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLoS Comput. Biol. 2017; 13:e1005575. PubMed PMC

Valasatava Y., Bradley A.R., Rose A.S., Duarte J.M., Prlić A., Rose P.W.. Towards an efficient compression of 3D coordinates of macromolecular structures. PLoS One. 2017; 12:e0174846. PubMed PMC

Sehnal D., Bittrich S., Velankar S., Koča J., Svobodová R., Burley S.K., Rose A.S.. BinaryCIF and CIFTools—lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 2020; 16:e1008247. PubMed PMC

Westbrook J.D., Fitzgerald P.M.D. Gu J., Bourne P.E.. Chapter 10 The PDB format, mmCIF formats, and other data formats. Structural Bioinformatics. 2009; Hoboken, New Jersey: Wiley-Blackwell; 271–291.

Cheng A., Henderson R., Mastronarde D., Ludtke S.J., Schoenmakers R.H.M., Short J., Marabini R., Dallakyan S., Agard D., Winn M. MRC2014: extensions to the MRC format header for electron cryo-microscopy and tomography. J. Struct. Biol. 2015; 192:146–150. PubMed PMC

Johnson G.T., Autin L., Al-Alusi M., Goodsell D.S., Sanner M.F., Olson A.J.. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat. Methods. 2015; 12:85–91. PubMed PMC

Sehnal D., Grant O.C.. Rapidly display glycan symbols in 3D structures: 3D-SNFG in LiteMol. J. Proteome Res. 2019; 18:770–774. PubMed

wwPDB consortium Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2019; 47:D520–D528. PubMed PMC

PDBe-KB consortium PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 2020; 48:D344–D353. PubMed PMC

Lawson C.L., Patwardhan A., Baker M.L., Hryc C., Garcia E.S., Hudson B.P., Lagerstedt I., Ludtke S.J., Pintilie G., Sala R.et al. .. EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 2016; 44:D396–D403. PubMed PMC

Lazar T., Martínez-Pérez E., Quaglia F., Hatos A., Chemes L.B., Iserte J.A., Méndez N.A., Garrone N.A., Saldaño T.E., Marchetti J.et al. .. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Res. 2021; 49:D404–D411. PubMed PMC

Piovesan D., Necci M., Escobedo N., Monzon A.M., Hatos A., Mičetić I., Quaglia F., Paladin L., Ramasamy P., Dosztányi Z.et al. .. MobiDB: intrinsically disordered proteins in 2021. Nucleic Acids Res. 2021; 49:D361–D367. PubMed PMC

Vedithi S.C., Malhotra S., Skwark M.J., Munir A., Acebrón-García-De-Eulate M., Waman V.P., Alsulami A., Ascher D.B., Blundell T.L.. HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. Comput. Struct. Biotechnol. J. 2020; 18:3692–3704. PubMed PMC

Doerr S., Harvey M.J., Noé F., De Fabritiis G.. HTMD: high-throughput molecular dynamics for molecular discovery. J. Chem. Theory Comput. 2016; 12:1845–1852. PubMed

Yu A., Pak A.J., He P., Monje-Galvan V., Casalino L., Gaieb Z., Dommer A.C., Amaro R.E., Voth G.A.. A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys. J. 2021; 120:1097–1104. PubMed PMC

Beliu G., Altrichter S., Guixà-González R., Hemberger M., Brauer I., Dahse A.-K., Scholz N., Wieduwild R., Kuhlemann A., Batebi H.et al. .. Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain. Mol. Cell. 2021; 81:905–921. PubMed

Grimme S., Bannwarth C., Shushkov P.. A robust and accurate tight-binding quantum chemical method for structures, vibrational frequencies, and noncovalent interactions of large molecular systems parametrized for all spd-block elements (Z = 1-86). J. Chem. Theory Comput. 2017; 13:1989–2009. PubMed

Manby F.R., Miller T.F. III, Bygrave P.J., Ding F., Dresselhaus T., Batista-Romero F.A., Buccheri A., Bungey C., Lee S.J.R., Meli R.et al. .. entos: a quantum molecular simulation package. 2019; ChemRxiv doi:26 February 2019, preprint: not peer reviewed10.26434/chemrxiv.7762646.v2. DOI

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