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  1. Book ; Online: Methods of Mapping Genetic Variability onto SARS-CoV-2 Protein Crystal Structures

    Yazdani, Setayesh / Schapira, Matthieu

    2020  

    Abstract: This post includes a step-by-step method for this post on openlabnotebook.org. ...

    Abstract This post includes a step-by-step method for this post on openlabnotebook.org.
    Keywords SARS-CoV-2 ; main protease structure ; Genetic variability ; covid19
    Publishing date 2020-05-19
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Genetic Variability at An Allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org. ...

    Abstract This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org.
    Keywords covid19
    Publishing date 2020-11-04
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Genetic Variability at An Allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org. ...

    Abstract This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org.
    Keywords covid19
    Publishing date 2020-11-04
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  4. Book ; Online: Druggability and Genetic Variability of the ATPase Site and Central Channel of SARS-CoV-2 nsp13 Helicase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and the genetic variability of the ATPase site and the central channel of SARS-CoV-2 nsp13 helicase across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks ... ...

    Abstract This document is about the druggability and the genetic variability of the ATPase site and the central channel of SARS-CoV-2 nsp13 helicase across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  5. Book ; Online: Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https:// ... ...

    Abstract This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  6. Book ; Online: Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https:// ... ...

    Abstract This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  7. Book ; Online: Methods-Calculating the change in Gibbs free energy (ddGbind) of inhibitor binding associated with genetic variations of SARS-CoV-2 Main Protease

    Yazdani, Setayesh / Schapira, Matthieu

    2020  

    Abstract: This method document accompanies the post on openlabnotebook.org here. In this document, we explain how we calculated the change in Gibbs free energy (ddGbind) of inhibitor binding associated with genetic variations of SARS-CoV-2 Main Protease. Nicola De ...

    Abstract This method document accompanies the post on openlabnotebook.org here. In this document, we explain how we calculated the change in Gibbs free energy (ddGbind) of inhibitor binding associated with genetic variations of SARS-CoV-2 Main Protease. Nicola De Maio provided a detailed method document for the work he did here prior to this step, which was investigating evolution at the catalytic site of the main SARS-CoV-2 protease using over 15,000 genomes.
    Keywords covid19
    Publishing date 2020-06-02
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  8. Article ; Online: Structure-based view of the druggable genome.

    Wang, Jiayan / Yazdani, Setayesh / Han, Ana / Schapira, Matthieu

    Drug discovery today

    2020  Volume 25, Issue 3, Page(s) 561–567

    Abstract: International efforts are underway to develop chemical probes for specific protein families, and a 'Target 2035' call to expand these efforts towards a comprehensive chemical coverage of the druggable human genome was recently announced. But what is the ... ...

    Abstract International efforts are underway to develop chemical probes for specific protein families, and a 'Target 2035' call to expand these efforts towards a comprehensive chemical coverage of the druggable human genome was recently announced. But what is the druggable genome? Here, we systematically review structures of proteins bound to drug-like ligands available from the Protein Data Bank (PDB) and use ligand desolvation upon binding as a druggability metric to draw a landscape of the human druggable genome. The vast majority of druggable protein families, including some highly populated and disease-associated families, are almost orphan of small-molecule ligands. We propose a list of 46 druggable domains representing 3440 human proteins that could be the focus of large chemical probe discovery efforts.
    MeSH term(s) Databases, Protein ; Drug Design ; Drug Discovery/methods ; Genome, Human ; Humans ; Ligands ; Protein Binding ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2020-02-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
    ZDB-ID 1324988-5
    ISSN 1878-5832 ; 1359-6446
    ISSN (online) 1878-5832
    ISSN 1359-6446
    DOI 10.1016/j.drudis.2020.02.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4725: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article: Genetic Variability of the SARS-CoV-2 Pocketome

    Yazdani, Setayesh / De Maio, Nicola / Ding, Yining / Shahani, Vijay / Goldman, Nick / Schapira, Matthieu

    Journal of proteome research. 2021 June 28, v. 20, no. 8

    2021  

    Abstract: In the absence of effective treatment, COVID-19 is likely to remain a global disease burden. Compounding this threat is the near certainty that novel coronaviruses with pandemic potential will emerge in years to come. Pan-coronavirus drugs—agents active ... ...

    Abstract In the absence of effective treatment, COVID-19 is likely to remain a global disease burden. Compounding this threat is the near certainty that novel coronaviruses with pandemic potential will emerge in years to come. Pan-coronavirus drugs—agents active against both SARS-CoV-2 and other coronaviruses—would address both threats. A strategy to develop such broad-spectrum inhibitors is to pharmacologically target binding sites on SARS-CoV-2 proteins that are highly conserved in other known coronaviruses, the assumption being that any selective pressure to keep a site conserved across past viruses will apply to future ones. Here we systematically mapped druggable binding pockets on the experimental structure of 15 SARS-CoV-2 proteins and analyzed their variation across 27 α- and β-coronaviruses and across thousands of SARS-CoV-2 samples from COVID-19 patients. We find that the two most conserved druggable sites are a pocket overlapping the RNA binding site of the helicase nsp13 and the catalytic site of the RNA-dependent RNA polymerase nsp12, both components of the viral replication–transcription complex. We present the data on a public web portal (https://www.thesgc.org/SARSCoV2_pocketome/), where users can interactively navigate individual protein structures and view the genetic variability of drug-binding pockets in 3D.
    Keywords COVID-19 infection ; RNA ; RNA-directed RNA polymerase ; Severe acute respiratory syndrome coronavirus 2 ; active sites ; burden of disease ; genetic variation ; pandemic ; proteome ; research
    Language English
    Dates of publication 2021-0628
    Size p. 4212-4215.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00206
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  10. Book ; Online: Genetic Variability at the Remdesivir-binding Pocket of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples

    Yazdani, Setayesh / De Maio, Nicola / Schapira, Matthieu

    2020  

    Abstract: In this document, we explain how we analyzed the genetic diversity at the remdesivir-binding site of RNA-dependent RNA Polymerase across coronaviruses and SARS-CoV-2 samples. This document accompanies posts 19 and 20 on openlabnotebook.org. ...

    Abstract In this document, we explain how we analyzed the genetic diversity at the remdesivir-binding site of RNA-dependent RNA Polymerase across coronaviruses and SARS-CoV-2 samples. This document accompanies posts 19 and 20 on openlabnotebook.org.
    Keywords covid19
    Publishing date 2020-09-21
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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