LeDock

LeDock
Original author(s)Lephar
Developer(s)Hongtao Zhao
Initial release12 June 2014; 10 years ago (2014-06-12) (Windows version)[1]
Written inC++
Operating systemLinux, macOS, and Windows
TypeMolecular docking
Websitewww.lephar.com/software.html

LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows.[2][3][4]

The software can run as a standalone programme or from Jupyter Notebook.[5] 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.[6][7][8][9][10] It is categorized as a flexible docking method.[11]

Performance

In a study involving 2,002 protein-ligand complexes, LeDock demonstrated a notable level of accuracy in predicting molecular poses. The Linux version contains command line tools to run automated virtual screening of different large molecular libraries in the cloud.[12][13]

In a performance evaluation of ten docking programs, LeDock demonstrated strong sampling power when compared against other commercial and academic alternatives.[14] 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

  1. ^ "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.
  2. ^ 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.
  3. ^ Zhao, Hongtao (2021). "User Guide for LeDock" (PDF). Lephar. Archived (PDF) from the original on June 15, 2022. Retrieved August 15, 2023.
  4. ^ "Applications of LeDock Software". Computational Biology Platform. CD ComputaBio. Retrieved August 15, 2023.
  5. ^ "Molecular docking — Chem-Workflows documentation". chem-workflows.com. Retrieved 2024-05-15.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.

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