Literature DB >> 34014278

3DBionotes COVID-19 Edition.

Jose Ramon Macias1, Ruben Sanchez-Garcia1, Pablo Conesa1, Erney Ramirez-Aportela1, Marta Martinez Gonzalez1, Carlos Wert-Carvajal1, Alberto M Parra-Perez1, Joan Segura Mora2, Sam Horrell3, Andrea Thorn4, Carlos O S Sorzano1, Jose Maria Carazo1.   

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: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy. AVAILABILITY: https://3dbionotes.cnb.csic.es/ws/covid19. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
© The Author(s) 2021. Published by Oxford University Press.

Entities:  

Year:  2021        PMID: 34014278      PMCID: PMC8241415          DOI: 10.1093/bioinformatics/btab397

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.931


  12 in total

1.  The SWISS-MODEL Repository-new features and functionality.

Authors:  Stefan Bienert; Andrew Waterhouse; Tjaart A P de Beer; Gerardo Tauriello; Gabriel Studer; Lorenza Bordoli; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

2.  3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations.

Authors:  Joan Segura; Ruben Sanchez-Garcia; C O S Sorzano; J M Carazo
Journal:  Bioinformatics       Date:  2019-09-15       Impact factor: 6.937

3.  DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps.

Authors:  Erney Ramírez-Aportela; Javier Mota; Pablo Conesa; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  IUCrJ       Date:  2019-09-18       Impact factor: 4.769

4.  FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation.

Authors:  Erney Ramírez-Aportela; David Maluenda; Yunior C Fonseca; Pablo Conesa; Roberto Marabini; J Bernard Heymann; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Nat Commun       Date:  2021-01-04       Impact factor: 14.919

5.  The PDB_REDO server for macromolecular structure model optimization.

Authors:  Robbie P Joosten; Fei Long; Garib N Murshudov; Anastassis Perrakis
Journal:  IUCrJ       Date:  2014-05-30       Impact factor: 4.769

6.  A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Authors:  Nicholas M Pearce; Tobias Krojer; Anthony R Bradley; Patrick Collins; Radosław P Nowak; Romain Talon; Brian D Marsden; Sebastian Kelm; Jiye Shi; Charlotte M Deane; Frank von Delft
Journal:  Nat Commun       Date:  2017-04-24       Impact factor: 14.919

7.  Structure of the Pandemic.

Authors:  Sarah Kearns
Journal:  Structure       Date:  2020-08-04       Impact factor: 5.006

8.  Measurement of atom resolvability in cryo-EM maps with Q-scores.

Authors:  Grigore Pintilie; Kaiming Zhang; Zhaoming Su; Shanshan Li; Michael F Schmid; Wah Chiu
Journal:  Nat Methods       Date:  2020-02-10       Impact factor: 28.547

9.  Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs.

Authors:  Atsushi Hijikata; Clara Shionyu-Mitsuyama; Setsu Nakae; Masafumi Shionyu; Motonori Ota; Shigehiko Kanaya; Tsuyoshi Shirai
Journal:  FEBS Lett       Date:  2020-05-25       Impact factor: 3.864

10.  Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

Authors:  Alice Douangamath; Daren Fearon; Paul Gehrtz; Tobias Krojer; Petra Lukacik; C David Owen; Efrat Resnick; Claire Strain-Damerell; Anthony Aimon; Péter Ábrányi-Balogh; José Brandão-Neto; Anna Carbery; Gemma Davison; Alexandre Dias; Thomas D Downes; Louise Dunnett; Michael Fairhead; James D Firth; S Paul Jones; Aaron Keeley; György M Keserü; Hanna F Klein; Mathew P Martin; Martin E M Noble; Peter O'Brien; Ailsa Powell; Rambabu N Reddi; Rachael Skyner; Matthew Snee; Michael J Waring; Conor Wild; Nir London; Frank von Delft; Martin A Walsh
Journal:  Nat Commun       Date:  2020-10-07       Impact factor: 14.919

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