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  1. Article ; Online: DockOpt: A Tool for Automatic Optimization of Docking Models.

    Knight, Ian S / Mailhot, Olivier / Tang, Khanh G / Irwin, John J

    Journal of chemical information and modeling

    2024  Volume 64, Issue 3, Page(s) 1004–1016

    Abstract: Molecular docking is a widely used technique for leveraging protein structure for ligand discovery, but it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress toward automation, docking still ... ...

    Abstract Molecular docking is a widely used technique for leveraging protein structure for ligand discovery, but it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress toward automation, docking still requires expert guidance, hindering its adoption by a broader range of investigators. To make docking more accessible, we developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens. DockOpt outperforms our previous automated pipeline across all 43 targets in the DUDE-Z benchmark data set, and the generated models for 84% of targets demonstrate sufficient enrichment to warrant their use in prospective screens, with normalized LogAUC values of at least 15%. DockOpt is available as part of the Python package Pydock3 included in the UCSF DOCK 3.8 distribution, which is available for free to academic researchers at https://dock.compbio.ucsf.edu and free for everyone upon registration at https://tldr.docking.org.
    MeSH term(s) Molecular Docking Simulation ; Prospective Studies ; Proteins/chemistry ; Ligands ; Benchmarking ; Protein Binding
    Chemical Substances Proteins ; Ligands
    Language English
    Publishing date 2024-01-11
    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.3c01406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Docking for Molecules That Bind in a Symmetric Stack with SymDOCK.

    Smith, Matthew S / Knight, Ian S / Kormos, Rian C / Pepe, Joseph G / Kunach, Peter / Diamond, Marc I / Shahmoradian, Sarah H / Irwin, John J / DeGrado, William F / Shoichet, Brian K

    Journal of chemical information and modeling

    2024  Volume 64, Issue 2, Page(s) 425–434

    Abstract: Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of great current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril ... ...

    Abstract Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of great current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures, the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein's symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand's docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural-network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in a
    MeSH term(s) Prospective Studies ; Ligands ; Retrospective Studies ; Proteins/chemistry ; Molecular Docking Simulation ; Protein Binding ; Binding Sites
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2024-01-08
    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.3c01749
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

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  3. Article: Docking for molecules that bind in a symmetric stack with SymDOCK.

    Smith, Matthew S / Knight, Ian S / Kormos, Rian C / Pepe, Joseph G / Kunach, Peter / Diamond, Marc I / Shahmoradian, Sarah H / Irwin, John J / DeGrado, William F / Shoichet, Brian K

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of much current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril ... ...

    Abstract Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of much current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein's symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand's docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in a
    Language English
    Publishing date 2023-10-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.27.564400
    Database MEDical Literature Analysis and Retrieval System OnLINE

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