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Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water

Title
Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water
Authors
Jung, Sang WonKim, Min SupRamsey, StevenKurtzman, TomCho, Art E.
DGIST Authors
정상원
Issue Date
2018-07
Citation
Scientific Reports, 8(1)
Type
Article
Article Type
Article
Keywords
ACTIVATED RECEPTOR-GAMMARETINOID-X-RECEPTORSPROTEIN DATA-BANKPOLY(ADP-RIBOSE) POLYMERASEGLUCOCORTICOID-RECEPTORBINDINGRECOGNITIONDOCKINGALGORITHMSAMBER
ISSN
2045-2322
Abstract
In this study, we demonstrate a method to construct a water-based pharmacophore model which can be utilized in the absence of known ligands. This method utilizes waters found in the binding pocket, sampled through molecular dynamics. Screening of compound databases against this water-based pharmacophore model reveals that this approach can successfully identify known binders to a target protein. The method was tested by enrichment studies of 7 therapeutically important targets and compared favourably to screening-by-docking with Glide. Our results suggest that even without experimentally known binders, pharmacophore models can be generated using molecular dynamics with waters and used for virtual screening. © 2018 The Author(s).
URI
http://hdl.handle.net/20.500.11750/9045
DOI
10.1038/s41598-018-28546-z
Publisher
Nature Publishing Group
Related Researcher
Files:
Collection:
Magnet-Controlled Materials Research Group1. Journal Articles


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