LeDock
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| Developer(s) | Lephar |
|---|---|
| Operating system | Cross-platform |
| Type | Molecular docking |
| Website | www |
LeDock is a simple proprietary molecular docking software that can be used for docking of ligands with protein target.[1] LeDock supports running on 64-bit Linux, macOS, and 32-bit and 64-bit Windows.
Introduction
LeDock is based on simulated annealing and evolutionary optimization of the ligand pose and its rotatable bonds, using a physics/knowledge-based scoring scheme derived from years of prospective virtual screening campaigns.[2][3][4][5][6]
Performance
LeDock had a good performance in a recent comprehensive evaluation of docking programs on a diverse set of 2002 protein-ligand complexes.[7] It has high accuracy in pose prediction, saving calculating time, and user friendly for both virtual screening and hit elaboration.
See also
- Drug design
- Macromolecular docking
- Molecular mechanics
- Protein structure
- Protein design
- Software for molecular mechanics modeling
- List of protein-ligand docking software
- Molecular design software
- Lead Finder
- Virtual screening
- Scoring functions for docking
References
- ^ "User Guide for LeDock" (PDF).
- ^ Zhao, Hongtao; Huang, Danzhi (2011-06-17). "Hydrogen Bonding Penalty upon Ligand Binding". PLOS ONE. 6 (6): e19923. doi:10.1371/journal.pone.0019923. ISSN 1932-6203. PMC 3117785. PMID 21698148.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Zhao, Hongtao; Huang, Danzhi; Caflisch, Amedeo (2012-11-01). "Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics". ChemMedChem. 7 (11): 1983–1990. doi:10.1002/cmdc.201200331. ISSN 1860-7187. PMID 22976951.
- ^ Zhao, Hongtao; Caflisch, Amedeo (2013-10-15). "Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics". Bioorganic & Medicinal Chemistry Letters. 23 (20): 5721–5726. doi:10.1016/j.bmcl.2013.08.009. PMID 23993776.
- ^ Zhao, Hongtao; Caflisch, Amedeo (2014-03-15). "Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk". Bioorganic & Medicinal Chemistry Letters. 24 (6): 1523–1527. doi:10.1016/j.bmcl.2014.01.083. PMID 24569110.
- ^ Zhao, Hongtao; Gartenmann, Lisa; Dong, Jing; Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014-06-01). "Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking". Bioorganic & Medicinal Chemistry Letters. 24 (11): 2493–2496. doi:10.1016/j.bmcl.2014.04.017. PMID 24767840.
- ^ Wang, Zhe (2016). "Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power". Physical Chemistry Chemical Physics. 18 (18): 12964–12975. doi:10.1039/C6CP01555G. PMID 27108770.