LeDock explained

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

• Drug design
• Macromolecular docking
• Molecular mechanics
• Molecular modelling
• Protein structure
• Protein design
• List of software for molecular mechanics modeling
• List of protein-ligand docking software
• Molecular design software
• Lead Finder
• Virtual screening
• Scoring functions for docking

External links

• Official website

Notes and References

1. Web site: 2014-06-12 . Lephar Research is pleased to announce the release of Windows version of LeDock . 2023-08-22 . Lephar Research (Archived). https://web.archive.org/web/20141217135453/http://lephar.com/ . 2014-12-17.
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 . . 18 . 18 . 12964–12975 . 2016PCCP...1812964W . 10.1039/C6CP01555G . 27108770 . 25603164 . RSC Publishing.
3. Web site: Zhao . Hongtao . 2021 . User Guide for LeDock . live . https://web.archive.org/web/20220615151705/http://www.lephar.com/download/LeDock.pdf . June 15, 2022 . August 15, 2023 . Lephar.
4. Web site: . . . Applications of LeDock Software . August 15, 2023 . Computational Biology Platform . CD ComputaBio.
5. Web site: Molecular docking — Chem-Workflows documentation . 2024-05-15 . chem-workflows.com.
6. Zhao . Hongtao . Huang . Danzhi . 2011-06-17 . Hydrogen Bonding Penalty upon Ligand Binding . PLOS ONE . en . 6 . 6 . e19923 . 10.1371/journal.pone.0019923 . free . 1932-6203 . 3117785 . 21698148. 2011PLoSO...619923Z .
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 . en . 7 . 11 . 1983–1990 . 10.1002/cmdc.201200331 . 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 . 10.1016/j.bmcl.2013.08.009 . 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 . 10.1016/j.bmcl.2014.01.083 . 24569110 . 0960-894X.
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 . 10.1016/j.bmcl.2014.04.017 . 0960-894X.
11. Fan . Jiyu . Fu . Ailing . Zhang . Le . June 2019 . Progress in molecular docking . Quantitative Biology . en . 7 . 2 . 83–89 . 10.1007/s40484-019-0172-y . 2095-4689. free .
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 . en . 18 . 18 . 12964–12975 . 10.1039/C6CP01555G . 2016PCCP...1812964W . 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 . 10.1088/1755-1315/218/1/012143 . 2019E&ES..218a2143L . 1755-1315. free .
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 . en . 18 . 18 . 12964–12975 . 10.1039/C6CP01555G . 2016PCCP...1812964W . 1463-9084.