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. 2021 Nov 18;37(22):4258-4260.
doi: 10.1093/bioinformatics/btab397.

3DBionotes COVID-19 edition

Jose Ramon Macias  1 , Ruben Sanchez-Garcia  1 , Pablo Conesa  1 , Erney Ramirez-Aportela  1 , Marta Martinez Gonzalez  1 , Carlos Wert-Carvajal  1 , Alberto M Parra-Perez  1 , Joan Segura Mora  2 , Sam Horrell  3 , Andrea Thorn  4 , Carlos O S Sorzano  1 , Jose Maria Carazo  1
Affiliations

3DBionotes COVID-19 edition

Jose Ramon Macias et al. Bioinformatics. .

Abstract

Summary: The web platform 3DBionotes-WS integrates multiple web services and an interactive web viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic electron microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context, we have developed 3DBionotes-COVID-19 as an answer to: (i) the need to explore multiomics data in a unified context with a special focus on structural information and (ii) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryo-EM.

Availability and implementation: https://3dbionotes.cnb.csic.es/ws/covid19.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
3DBionotes COVID-19 application screenshots. (A) Landing page, showing some of the main sections: representative examples, a simplified schema of the virus proteome that serves as index with links to the corresponding subsection for every protein, followed by various panels with the structures. (B) 3D viewer and annotations, showing the example of EMD-21452, corresponding to SARS-CoV-2 spike glycoprotein (closed state). By clicking in any of the symbols representing an annotation, all the residues associated with it will be highlighted in the protein sequence alignment as well as in the atomic structure. At the same time, those residues will also be highlighted with vertical yellow bars so it is easier to locate in relation with other annotations types. Additionally, a panel will pop-up with more detailed information about the annotation, including links to the origin of the data source
See this image and copyright information in PMC

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