Docking software performance in protein-glycosaminoglycan systems
PBN-AR
Instytucja
Wydział Chemii (Uniwersytet Gdański)
Informacje podstawowe
Główny język publikacji
en
Czasopismo
Journal of Molecular Graphics & Modelling
ISSN
1093-3263
EISSN
Wydawca
DOI
URL
Rok publikacji
2019
Numer zeszytu
Strony od-do
42-50
Numer tomu
90
Identyfikator DOI
Liczba arkuszy
0.5
Autorzy
Pozostali autorzy
+ 1
Słowa kluczowe
en
molecular docking
protein-glycosaminoglycan interactions
modeling glycosaminoglycans
scoring function
binding pose
Streszczenia
Język
en
Treść
We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned. Our results suggest that Dock program performs best in terms of the pose placement, has the most suitable scoring function, and its performance did not depend on the ligand size. This suggests that the implementation of the electrostatics as well as the shape complementarity procedure in Dock are the most suitable for docking glycosaminoglycan ligands. We also analyzed how free energy patterns of the benchmarking complexes affect the performance of the evaluated docking software.
Inne
System-identifier
UOG86138e4a325c415ca2f4e2d1f8ee62e6
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