NGL viewer: web-based molecular graphics for large complexes

Rose, Alexander; Bradley, A.R.; Valasatava, Yana; Duarte, José M.; Prlić, Andreas; Rose, Peter W.

doi:10.1093/bioinformatics/bty419

Cited by 407 publications

(347 citation statements)

References 20 publications

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“…A Basic Local Alignment Search Tool (BLAST) was employed by the Data Bank to identify the most identical crystalized protein structure to the subject protein sequence. Then, the NMR structure for the most identical crystalized protein structure would be visualized by NGL (WebGL) viewer [79].…”

Section: Protein Modellingmentioning

confidence: 99%

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

2020

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Background: Coronavirus disease 2019 is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies. Results: In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Then through the computational modelling and antigenicity prediction approaches, the identified polyprotein sequence was analyzed. The results revealed that the identified ORF1ab polyprotein belongs to a part of nonstructural protein 1 (nsp1) with the high antigenicity residues in a glycine-proline or hydrophobic amino acid rich domain. Conclusions:The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies.

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Section: Protein Modellingmentioning

confidence: 99%

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

2020

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“…J. P. Daniel Therien is thanked for his help with the preparation of Figure 6 B. The ribbon‐like schematic of a protein in the Table of Contents and Frontispiece was drawn using NGL viewer, based on the crystal structure of CALB (PDB ID: 4K6G), published by Xie et al. [180]…”

Section: Acknowledgementsmentioning

confidence: 99%

“…Writing of this article and our research in this area were funded by the McGill Sustainability SystemsI nitiativeI nnovation Grant, an IHC4a ward from the GreenCentre Canada, and NSERC grants (RGPIN-2017-06467,S MFSU 507347-17). J. P. Daniel Therien is thanked for his help with the preparation of Figure 6B.T he ribbon-like schematic of ap rotein in the Table of Contents and Frontispiece was drawn using NGL viewer, [179] based on the crystal structureofC ALB (PDB ID:4K6G),published by Xie et al [180]…”

Section: Acknowledgementsmentioning

confidence: 99%

Mechanoenzymatic Transformations in the Absence of Bulk Water: A More Natural Way of Using Enzymes

2019

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Mechanochemical enzymatic reactions without bulk water have emerged as a low‐waste and efficient method to access useful chemicals and to depolymerize biomass components in a single step. This emergent mechanoenzymatic reaction strategy is able to take advantage of the stereospecificity, regio‐ and stereoselectivity, as well as renewability of enzymes, while avoiding bulk solvents, offering the opportunity to control the direction of the reaction, bypassing reactant solubility issues, and enabling reactions with water‐sensitive substrates or products. Enzymes are traditionally used in dilute aqueous solution, which is quite different from their crowded, water‐depleted natural environment. This review outlines recent work which demonstrates that enzymes can be equally or even more efficient under mechanochemical conditions, without bulk aqueous or organic solvent.

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“…A–C were generated with NGL Viewer (Rose et al . ), D–E are from Schmidt et al . (); scale bars represent 10 µm.…”

Section: Inflammasomesmentioning

confidence: 99%

From atoms to physiology: what it takes to really understand inflammasomes

Schmidt

2019

The Journal of Physiology

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Rapid inflammatory responses to cytosolic threats are mediated by inflammasomes – large macromolecular signalling complexes that control the activation of the pro‐inflammatory cytokines interleukin (IL)‐1β and IL‐18, as well as cell death by pyroptosis. Different inflammasome sensors are activated by diverse direct and indirect signals, and subsequently nucleate the polymerization of the adaptor molecule ASC to form signalling platforms macroscopically observed as ASC specks. Caspase‐1 is autocatalytically activated at these sites and subsequently matures pro‐inflammatory cytokines and the pore‐forming effector molecule gasdermin D. While most molecules and basic assembly principles have been deduced from reductionist experimental systems, we still lack fundamental information on the structure and regulation of these complexes in their physiological environment and in the interplay with other signalling pathways. In this review, novel experimental approaches are proposed, including some that rely on nanobodies and single domain antibodies, to understand inflammasome assembly and regulation in the context of the relevant tissues or cells.

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NGL viewer: web-based molecular graphics for large complexes

Abstract: The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript.

Cited by 407 publications

References 20 publications

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

Mechanoenzymatic Transformations in the Absence of Bulk Water: A More Natural Way of Using Enzymes

From atoms to physiology: what it takes to really understand inflammasomes

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