LeDock
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| LeDock | |
|---|---|
| Original author | Lephar |
| Developer | Hongtao Zhao |
| Release | 12 June 2014 (Windows version) |
| Written in | C++ |
| Operating system | Linux, macOS, and Windows |
| Type | Molecular docking |
| Website | www |
LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows.
The software can run as a standalone programme or from Jupyter Notebook. It supports the Tripos Mol2 file format.
Methodology
LeDock utilizes a simulated annealing and genetic algorithm approach for facilitating the docking process of ligands with protein targets. The software employs a knowledge-based scoring scheme that is derived from extensive prospective virtual screening campaigns. It is categorized as a flexible docking method.
Performance
In a study involving 2,002 protein-ligand complexes, LeDock was repoted to have high sampling power. The Linux version contains command line tools to run automated virtual screening of different large molecular libraries in the cloud.
In a performance evaluation of ten docking programs, LeDock demonstrated strong sampling power when compared against other commercial and academic alternatives. According to a review from 2017, LeDock was noted for its effectiveness in sampling ligand conformational space, identifying near-native binding poses, and having a flexible docking protocol. The Linux version includes tools for high-throughput virtual screening in the cloud.
See also
References
- ↑ "Lephar Research is pleased to announce the release of Windows version of LeDock". Lephar Research (Archived). 2014-06-12. Archived from the original on 2014-12-17. Retrieved 2023-08-22.
- ↑ Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T (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. Bibcode:2016PCCP...1812964W. doi:10.1039/C6CP01555G. PMID 27108770. S2CID 25603164 – via RSC Publishing.
- ↑ Zhao, Hongtao (2021). "User Guide for LeDock" (PDF). Lephar. Archived (PDF) from the original on June 15, 2022. Retrieved August 15, 2023.
- ↑ "Applications of LeDock Software". Computational Biology Platform. CD ComputaBio. Retrieved August 15, 2023.
- ↑ "Molecular docking — Chem-Workflows documentation". chem-workflows.com. Retrieved 2024-05-15.
- ↑ Zhao, Hongtao; Huang, Danzhi (2011-06-17). "Hydrogen Bonding Penalty upon Ligand Binding". PLOS ONE. 6 (6) e19923. Bibcode:2011PLoSO...619923Z. doi:10.1371/journal.pone.0019923. ISSN 1932-6203. PMC 3117785. PMID 21698148.
- ↑ Zhao, Hongtao; Huang, Danzhi; Caflisch, Amedeo (November 2012). "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 1860-7179. 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. ISSN 0960-894X. 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. ISSN 0960-894X. 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. ISSN 0960-894X. PMID 24767840.
- ↑ Fan, Jiyu; Fu, Ailing; Zhang, Le (June 2019). "Progress in molecular docking". Quantitative Biology. 7 (2): 83–89. doi:10.1007/s40484-019-0172-y. ISSN 2095-4689.
- ↑ Wang, Zhe; Sun, Huiyong; Yao, Xiaojun; Li, Dan; Xu, Lei; Li, Youyong; Tian, Sheng; Hou, Tingjun (2016-05-04). "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. Bibcode:2016PCCP...1812964W. doi:10.1039/C6CP01555G. ISSN 1463-9084. PMID 27108770.
- ↑ Liu, Ni; Xu, Zhibin (2019-02-23). "Using LeDock as a docking tool for computational drug design". IOP Conference Series: Earth and Environmental Science. 218 (1) 012143. Bibcode:2019E&ES..218a2143L. doi:10.1088/1755-1315/218/1/012143. ISSN 1755-1315.
- ↑ Wang, Zhe; Sun, Huiyong; Yao, Xiaojun; Li, Dan; Xu, Lei; Li, Youyong; Tian, Sheng; Hou, Tingjun (2016-05-04). "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. Bibcode:2016PCCP...1812964W. doi:10.1039/C6CP01555G. ISSN 1463-9084. PMID 27108770.
- Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T (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 27108765.
- Shen M, Zhou S, Li Y, Pan P, Li D, Hou T (2020). "Discovery of potent inhibitors for the inhibition of protein–protein interactions: a comprehensive review and benchmark of the state-of-the-art". Briefings in Bioinformatics. 21 (4): 1413–1432. doi:10.1093/bib/bbz097. PMC 7673343. PMID 31359048.
- Bouchouireb Z, Boulahtouf A, Khier S, Ouassat M, Oukkache N (2024). "In silico assessment of neonicotinoid pesticides binding to nicotinic acetylcholine receptors: a comparative docking study". Ecotoxicology and Environmental Safety. 279 116484. doi:10.1016/j.ecoenv.2024.116484.