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  1. Article ; Online: Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease.

    Sztain, Terra / Amaro, Rommie / McCammon, J Andrew

    Journal of chemical information and modeling

    2021  Volume 61, Issue 7, Page(s) 3495–3501

    Abstract: The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern ...

    Abstract The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on
    MeSH term(s) COVID-19 ; Catalytic Domain ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; Protease Inhibitors ; SARS-CoV-2 ; Viral Proteins
    Chemical Substances Protease Inhibitors ; Viral Proteins ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2021-05-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.1c00140
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease

    Sztain, Terra / Amaro, Rommie E / McCammon, James Andrew

    bioRxiv

    Abstract: ... we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far ... The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern ... from the active site and assed their druggability. These pockets can aid in virtual screening efforts to identify ...

    Abstract The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site and assed their druggability. These pockets can aid in virtual screening efforts to identify a protease inhibitor for the treatment of COVID-19.
    Keywords covid19
    Language English
    Publishing date 2020-07-24
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.07.23.218784
    Database COVID19

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