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Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK

  1. Author:
    Chakrabarti,Mayukh
    Tan, Y Stanley
    Balius,Trent

  2. Author Address

    NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. trent.balius@nih.gov.,
    1. Year: 2024
  2. Journal: Methods in Molecular Biology (Clifton, N.J.)
    1. 2797
    2. Pages: 67-90
  4. Type of Article: Article
  1. Abstract:

    Molecular docking is a popular computational tool in drug discovery. Leveraging structural information, docking software predicts binding poses of small molecules to cavities on the surfaces of proteins. Virtual screening for ligand discovery is a useful application of docking software. In this chapter, using the enigmatic KRAS protein as an example system, we endeavor to teach the reader about best practices for performing molecular docking with UCSF DOCK. We discuss methods for virtual screening and docking molecules on KRAS. We present the following six points to optimize our docking setup for prosecuting a virtual screen: protein structure choice, pocket selection, optimization of the scoring function, modification of sampling spheres and sampling procedures, choosing an appropriate portion of chemical space to dock, and the choice of which top scoring molecules to pick for purchase. © 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

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External Sources

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  2. DOI: 10.1007/978-1-0716-3822-4_6
  3. PMID: 38570453

Library Notes

  1. Fiscal Year: FY2023-2024
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