These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: Simplified AutoDock force field for hydrated binding sites.
    Author: Wojciechowski M.
    Journal: J Mol Graph Model; 2017 Nov; 78():74-80. PubMed ID: 29054096.
    Abstract:
    A set of high quality structures of protein-ligand complexes with experimentally determined binding affinities has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more.
    [Abstract] [Full Text] [Related] [New Search]