Docking software performance in protein-glycosaminoglycan systems

Urszula Uciechowska-Kaczmarzyk , Isaure Chauvot de Beauchene , Sergey Samsonov

Abstract

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.
Author Urszula Uciechowska-Kaczmarzyk (FCh / DTCh / LMM)
Urszula Uciechowska-Kaczmarzyk,,
- Laboratory of Molecular Modeling
, Isaure Chauvot de Beauchene
Isaure Chauvot de Beauchene,,
-
, Sergey Samsonov (FCh / DTCh / LMM)
Sergey Samsonov,,
- Laboratory of Molecular Modeling
Journal seriesJournal of Molecular Graphics & Modelling, ISSN 1093-3263, (A 25 pkt)
Issue year2019
Vol90
Pages42-50
Publication size in sheets0.5
Keywords in Englishmolecular docking, protein-glycosaminoglycan interactions, modeling glycosaminoglycans, scoring function, binding pose
ASJC Classification2505 Materials Chemistry; 1704 Computer Graphics and Computer-Aided Design; 1606 Physical and Theoretical Chemistry; 1607 Spectroscopy
DOIDOI:10.1016/j.jmgm.2019.04.001
URL https://doi.org/10.1016/j.jmgm.2019.04.001
Languageen angielski
Score (nominal)25
ScoreMinisterial score = 25.0, 24-07-2019, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.735; WoS Impact Factor: 2017 = 1.885 (2) - 2017=1.806 (5)
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