Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database
The number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it has increased tenfold in the last twenty years. The availability of an ever-growing number of structures is having a huge impact on the Structure-Based Drug Discovery (SBDD), allowing investigation of new tar...
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doaj-ce51394ab91e4b4db647cfba228ee6712020-11-24T20:53:43ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-07-012014355810.3390/ijms20143558ijms20143558Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind DatabaseGiovanni Bolcato0Alberto Cuzzolin1Maicol Bissaro2Stefano Moro3Mattia Sturlese4Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, ItalyMolecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, ItalyMolecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, ItalyMolecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, ItalyMolecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, ItalyThe number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it has increased tenfold in the last twenty years. The availability of an ever-growing number of structures is having a huge impact on the Structure-Based Drug Discovery (SBDD), allowing investigation of new targets and giving the possibility to have multiple structures of the same macromolecule in a complex with different ligands. Such a large resource often implies the choice of the most suitable complex for molecular docking calculation, and this task is complicated by the plethora of possible posing and scoring function algorithms available, which may influence the quality of the outcomes. Here, we report a large benchmark performed on the PDBbind database containing more than four thousand entries and seventeen popular docking protocols. We found that, even in protein families wherein docking protocols generally showed acceptable results, certain ligand-protein complexes are poorly reproduced in the self-docking procedure. Such a trend in certain protein families is more pronounced, and this underlines the importance in identification of a suitable protein−ligand conformation coupled to a well-performing docking protocol.https://www.mdpi.com/1422-0067/20/14/3558molecular dockingdocking benchmarkDockBenchvirtual screening |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Giovanni Bolcato Alberto Cuzzolin Maicol Bissaro Stefano Moro Mattia Sturlese |
spellingShingle |
Giovanni Bolcato Alberto Cuzzolin Maicol Bissaro Stefano Moro Mattia Sturlese Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database International Journal of Molecular Sciences molecular docking docking benchmark DockBench virtual screening |
author_facet |
Giovanni Bolcato Alberto Cuzzolin Maicol Bissaro Stefano Moro Mattia Sturlese |
author_sort |
Giovanni Bolcato |
title |
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
title_short |
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
title_full |
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
title_fullStr |
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
title_full_unstemmed |
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
title_sort |
can we still trust docking results? an extension of the applicability of dockbench on pdbbind database |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2019-07-01 |
description |
The number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it has increased tenfold in the last twenty years. The availability of an ever-growing number of structures is having a huge impact on the Structure-Based Drug Discovery (SBDD), allowing investigation of new targets and giving the possibility to have multiple structures of the same macromolecule in a complex with different ligands. Such a large resource often implies the choice of the most suitable complex for molecular docking calculation, and this task is complicated by the plethora of possible posing and scoring function algorithms available, which may influence the quality of the outcomes. Here, we report a large benchmark performed on the PDBbind database containing more than four thousand entries and seventeen popular docking protocols. We found that, even in protein families wherein docking protocols generally showed acceptable results, certain ligand-protein complexes are poorly reproduced in the self-docking procedure. Such a trend in certain protein families is more pronounced, and this underlines the importance in identification of a suitable protein−ligand conformation coupled to a well-performing docking protocol. |
topic |
molecular docking docking benchmark DockBench virtual screening |
url |
https://www.mdpi.com/1422-0067/20/14/3558 |
work_keys_str_mv |
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