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Tytuł pozycji:

Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.

Tytuł:
Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.
Autorzy:
Guterres H; Department of Biological Sciences , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.
Lee HS; Department of Biological Sciences , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.
Im W; Department of Biological Sciences , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.; School of Computational Sciences , Korea Institute for Advanced Study , Seoul 02455 , Republic of Korea.
Źródło:
Journal of chemical theory and computation [J Chem Theory Comput] 2019 Nov 12; Vol. 15 (11), pp. 6524-6535. Date of Electronic Publication: 2019 Oct 14.
Typ publikacji:
Journal Article
Język:
English
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
MeSH Terms:
Ligands*
Molecular Docking Simulation*
Proteins/*chemistry
Binding Sites ; Protein Structure, Tertiary
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Grant Information:
R01 GM126140 United States GM NIGMS NIH HHS
Substance Nomenclature:
0 (Ligands)
0 (Proteins)
Entry Date(s):
Date Created: 20190927 Date Completed: 20191120 Latest Revision: 20191204
Update Code:
20240105
PubMed Central ID:
PMC6884403
DOI:
10.1021/acs.jctc.9b00751
PMID:
31557013
Czasopismo naukowe
Accurate modeling of ligand-binding-site structures plays a critical role in structure-based virtual screening. However, the structures of the ligand-binding site in most predicted protein models are generally of low quality and need refinements. In this work, we present a ligand-binding-site structure refinement protocol using molecular dynamics simulation with restraints derived from predicted binding site templates. Our benchmark validation shows great performance for 40 diverse sets of proteins from the Astex list. The ligand-binding sites on modeled protein structures are consistently refined using our method with an average Cα RMSD improvement of 0.90 Å. Comparison of ligand binding modes from ligand docking to initial unrefined and refined structures shows an average of 1.97 Å RMSD improvement in the refined structures. These results demonstrate a promising new method of structure refinement for protein ligand-binding-site structures.

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