Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database
| العنوان: | Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database |
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| المؤلفون: | Maicol Bissaro, Stefano Moro, Giovanni Bolcato, Mattia Sturlese, Alberto Cuzzolin |
| المصدر: | International Journal of Molecular Sciences, Vol 20, Iss 14, p 3558 (2019) International Journal of Molecular Sciences Volume 20 Issue 14 |
| بيانات النشر: | MDPI AG, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | DockBench, 0301 basic medicine, 030103 biophysics, Computer science, Protein Data Bank (RCSB PDB), computer.software_genre, Article, Catalysis, lcsh:Chemistry, Inorganic Chemistry, 03 medical and health sciences, Physical and Theoretical Chemistry, Databases, Protein, lcsh:QH301-705.5, Molecular Biology, Spectroscopy, Virtual screening, Database, Drug discovery, Organic Chemistry, molecular docking, General Medicine, computer.file_format, virtual screening, Protein Data Bank, docking benchmark, Computer Science Applications, Molecular Docking Simulation, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, Docking (molecular), computer |
| الوصف: | 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&ndash ligand conformation coupled to a well-performing docking protocol. |
| وصف الملف: | application/pdf |
| تدمد: | 1422-0067 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4789d952d3ab8b4a7c7123a90703d5b4 https://doi.org/10.3390/ijms20143558 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....4789d952d3ab8b4a7c7123a90703d5b4 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14220067 |
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