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Browsing by Author Zaidman, Daniel

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  • OER000000215.pdf.jpg
  • Journal article

  • An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor

    • Authors : Zaidman, Daniel; Gehrtz, Paul; Filep, Mihajlo (2020)

  • Present covalentizer, a computational pipeline for creating irreversible inhibitors based on complex structures of targets with known reversible binders. For each ligand, we create a custom-made focused library of covalent analogs. We use covalent docking, to dock these tailored covalent libraries and to find those that can bind covalently to a nearby cysteine while keeping some of the main interactions of the original molecule. We found ~11,000 cysteine...
  • OER000000404.pdf.jpg
  • Journal article

  • PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes

    • Authors : Zaidman, Daniel; London, Nir (2020)

  • Proteolysis-targeting chimeras (PROTACs), which induce degradation by recruitment of an E3 ligase to a target protein, are gaining much interest as a new pharmacological modality. However, designing PROTACs is challenging. Formation of a ternary complex between the protein target, the PROTAC and the recruited E3 ligase is considered paramount for successful degradation. A structural model of this ternary complex could in principle inform rational PROTAC design.&#x...