LeDock

LeDock is a proprietary, flexible molecular docking software designed for the purpose of docking ligands with target proteins. It is available for Linux, macOS, and Windows.[2][3][4]

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

It can be ran as a standalone program or entirely from Jupyter notebook.[5] It supports only the Tripos Mol2 file format - which is a file format commonly used in computational chemistry and molecular modeling.[6]

Introduction

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.[7][8][9][10][11] It is categorized as using a flexible docking method.[12]

Performance

Performance: In a comprehensive study involving 2002 protein-ligand complexes, LeDock demonstrated a notable level of accuracy in predicting molecular poses. Moreover, the Linux version offers command line tools to run high-throughput virtual screening of different large molecular libraries in the cloud.[2][13][6]

In a computational study screening for inhibitors of Mycobacterium tuberculosis DNA gyrase B, LeDock demonstrated better performance than AutoDock Vina at reproducing experimental binding affinity data. When benchmarked on a set of 140 known gyrase inhibitors, the predicted binding energies from LeDock docking experiments showed a significantly higher correlation to experimental inhibition constant (pKi) values compared to Vina. Docking software efficacy varies by target site, so running experimental benchmarks when choosing a docking software is advised.[14]

A 2017 review evaluated the accuracy of different docking software on a diverse set of protein-ligand complexes. LeDock was able to effectively sample ligand conformational space and identify near-native binding poses for a significant proportion of the test cases. Its flexible docking protocol was pointed out as a key factor for accurate docking.[15]

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. Moreno, Angel J. Ruiz (2021-09-18). "Molecular Docking". Cheminformatics Workflows. Retrieved 2023-08-08.
  6. "生信云实证Vol.12：王者带飞LeDock！开箱即用分子库+全流程自动" [Bioinformatics Cloud Proof Vol.12: Leading with LeDock! Plug-and-Play Molecular Library + Full Automated Workflow]. baijiahao.baidu.com. 2022-09-13. Retrieved 2023-08-09.
  7. 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.
  8. 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. S2CID 16545198.
  9. 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.
  10. 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.
  11. 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.
  12. Fan, Jiyu; Fu, Ailing; Zhang, Le (2019). "Progress in molecular docking". Quantitative Biology. 7 (2): 83–89. doi:10.1007/s40484-019-0172-y. ISSN 2095-4689.
  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. Arévalo, Juan Marcelo Carpio; Amorim, Juliana Carolina (2022-03-18). "Virtual screening, optimization and molecular dynamics analyses highlighting a pyrrolo[1,2-a]quinazoline derivative as a potential inhibitor of DNA gyrase B of Mycobacterium tuberculosis". Scientific Reports. 12 (1): 4742. Bibcode:2022NatSR..12.4742A. doi:10.1038/s41598-022-08359-x. PMC 8933452. PMID 35304513.
  15. Pagadala, Nataraj S.; Syed, Khajamohiddin; Tuszynski, Jack (April 2017). "Software for molecular docking: a review". Biophysical Reviews. 9 (2): 91–102. doi:10.1007/s12551-016-0247-1. ISSN 1867-2450. PMC 5425816. PMID 28510083.
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