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Title: GitHub - omicscodeathon/denguedrug: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus · GitHub

Open Graph Title: GitHub - omicscodeathon/denguedrug: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus

X Title: GitHub - omicscodeathon/denguedrug: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus

Description: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus - omicscodeathon/denguedrug

Open Graph Description: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus - omicscodeathon/denguedrug

X Description: Machine Learning and Molecular Docking Prediction of Potential Inhibitors against Dengue Virus - omicscodeathon/denguedrug

Mail addresses
george.hanson417@gmail.com
jkojoadams@gmail.com
davesonbrank@gmail.com
asanteandy65@gmail.com
hembondarwad@gmail.com
maureenkisaakye6@gmail.com
lewistem8@gmail.com
sohamshirolkar@gmail.com
laitanawe@gmail.com

Opengraph URL: https://github.com/omicscodeathon/denguedrug

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README.mdhttps://github.com/omicscodeathon/denguedrug/blob/main/README.md
READMEhttps://github.com/omicscodeathon/denguedrug
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https://GitHub.com/omicscodeathon/denguedrug/graphs/contributors/
https://github.com/omicscodeathon/denguedrug/tags/
https://github.com/omicscodeathon/denguedrug#denguedrug
https://github.com/omicscodeathon/denguedrug#overview
pipelinehttps://github.com/omicscodeathon/denguedrug#workflow-diagram
descriptionhttps://github.com/omicscodeathon/denguedrug#description-section
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https://github.com/omicscodeathon/denguedrug#table-of-contents
Objectiveshttps://github.com/omicscodeathon/denguedrug#objectives
Descriptionhttps://github.com/omicscodeathon/denguedrug#description
Identification of Dengue Virus inhibitors database for ML traininghttps://github.com/omicscodeathon/denguedrug#step-1-identification-of-dengue-virus-inhibitors-database-for-ml-training
Preprocessinghttps://github.com/omicscodeathon/denguedrug#step-2-preprocessing
Model constructionhttps://github.com/omicscodeathon/denguedrug#step-3-model-construction
Predictionhttps://github.com/omicscodeathon/denguedrug#step-4-prediction
Molecular Dockinghttps://github.com/omicscodeathon/denguedrug#step-5-molecular-docking
ADMET predictionhttps://github.com/omicscodeathon/denguedrug#step-6-admet-prediction
Molecular Dynamics (MD) Simulationshttps://github.com/omicscodeathon/denguedrug#step-7-molecular-dynamics-md-simulations
Manuscripthttps://github.com/omicscodeathon/denguedrug#manuscript
Resultshttps://github.com/omicscodeathon/denguedrug#results
Data Acquisition and Processinghttps://github.com/omicscodeathon/denguedrug#data-acquisition-and-processing
Model Development and Evaluationhttps://github.com/omicscodeathon/denguedrug#model-development-and-evaluation
Prediction of Inhibitors and Compoundshttps://github.com/omicscodeathon/denguedrug#prediction-of-inhibitors-and-new-compounds
Target Selection and Molecular Docking of Predicted Compoundshttps://github.com/omicscodeathon/denguedrug#target-selection-and-molecular-docking-of-predicted-compounds
Mechanism of Binding Characterization of Selected Compoundshttps://github.com/omicscodeathon/denguedrug#mechanism-of-binding-characterization-of-selected-compounds
ADMET Screening of Selected Compoundshttps://github.com/omicscodeathon/denguedrug#admet-screening-of-selected-compounds
Molecular Dynamics Simulationshttps://github.com/omicscodeathon/denguedrug#molecular-dynamics-simulations
MMPBSA Computationshttps://github.com/omicscodeathon/denguedrug#mmpbsa-computations
How to usehttps://github.com/omicscodeathon/denguedrug#how-to-use
Data Availabilityhttps://github.com/omicscodeathon/denguedrug#data-availability
Reproducibility Prerequisiteshttps://github.com/omicscodeathon/denguedrug#reproducibility-prerequisites
Creditshttps://github.com/omicscodeathon/denguedrug#credits
https://github.com/omicscodeathon/denguedrug#objectives
https://github.com/omicscodeathon/denguedrug#description
https://github.com/omicscodeathon/denguedrug/blob/main/workflow/DengueDrug%20project%20workflow%20diagram.png
https://github.com/omicscodeathon/denguedrug#step-1-identification-of-dengue-virus-inhibitors-database-for-ml-training
BioAssay ID: 651640https://pubchem.ncbi.nlm.nih.gov/bioassay/651640
Broad Institutehttp://www.broadinstitute.org/
https://github.com/omicscodeathon/denguedrug#step-2-preprocessing
herehttps://github.com/omicscodeathon/denguedrug/blob/main/data/unprocessed_database_PubChem_651640
activeshttps://github.com/omicscodeathon/denguedrug/blob/main/data/Actives.smi
inactivehttps://github.com/omicscodeathon/denguedrug/blob/main/data/Inactives.smi
PaDEL-Descriptorshttp://www.yapcwsoft.com/dd/padeldescriptor/
actives and inactiveshttps://github.com/omicscodeathon/denguedrug/blob/main/data
Descriptor Calculatorhttps://github.com/omicscodeathon/denguedrug/blob/main/scripts/DescriptorCalculator.py
metricshttps://github.com/omicscodeathon/denguedrug/blob/main/data/metrics.csv
https://github.com/omicscodeathon/denguedrug#step-3-model-construction
traininghttps://github.com/omicscodeathon/denguedrug/blob/main/data/Training%20Data.csv.zip
testhttps://github.com/omicscodeathon/denguedrug/blob/main/data/Test%20Data.csv
externalhttps://github.com/omicscodeathon/denguedrug/blob/main/data/External%20Data.csv
lazy predicthttps://github.com/shankarpandala/lazypredict
metricshttps://github.com/omicscodeathon/denguedrug/blob/main/figures/Lazy_predict_results.jpeg
modelshttps://github.com/omicscodeathon/denguedrug/blob/main/output/models
selection metricshttps://github.com/omicscodeathon/denguedrug/blob/main/ML_results_for_model_selection.jpeg
evaluation metricshttps://github.com/omicscodeathon/denguedrug/blob/main/figures/Model_selection_results_on_test_dataset.png
https://github.com/omicscodeathon/denguedrug#step-4-prediction
Northern African Natural Products Database (NANPD)https://african-compounds.org/about/nanpdb/
East African Natural Products Database (EANPD)https://african-compounds.org/about/eanpdb/
AfroDBhttps://african-compounds.org/about/afrodb/
Tradtional Chinese Medicine (TCM) databasehttp://tcm.cmu.edu.tw/about01.php?menuid=1
https://github.com/omicscodeathon/denguedrug#step-5-molecular-docking
PDB: 2FOMhttps://doi.org/10.2210/pdb2FOM/pdb
AutoDock Vinahttps://vina.scripps.edu
LigPlot + v1.4.5https://doi.org/10.1021/ci200227u
https://github.com/omicscodeathon/denguedrug#step-6-admet-prediction
SwissADMEhttp://www.swissadme.ch
Veber's rulehttps://doi.org/10.3390/molecules25020321
Lipinski's Rule of Fivehttps://doi.org/10.1016/j.drudis.2019.10.014
https://github.com/omicscodeathon/denguedrug#step-7-molecular-dynamics-md-simulations
GROMACShttps://doi.org/10.1021/ci500020m
Xmgracehttps://doi.org/10.1163/_q3_SIM_00374
ProLIFhttps://prolif.readthedocs.io/en/stable/
Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA)https://doi.org/10.1021/ci500020m
https://github.com/omicscodeathon/denguedrug#manuscript
citehttps://x.com/natfriedman/status/1420122675813441540/photo/1
starhttps://docs.github.com/en/get-started/exploring-projects-on-github/saving-repositories-with-stars
https://github.com/omicscodeathon/denguedrug#results
https://github.com/omicscodeathon/denguedrug#data-acquisition-and-processing
bioactive datasethttps://github.com/omicscodeathon/denguedrug/blob/main/data/unprocessed_database_PubChem_651640/DENV2_PubChem_database_AID_651640_datatable.csv
PubChemhttps://pubchem.ncbi.nlm.nih.gov/
Figure 1https://github.com/omicscodeathon/denguedrug#figure-1
PaDELhttps://doi.org/10.1002/jcc.21707
14,875 training sethttps://github.com/omicscodeathon/denguedrug/blob/main/data/Training Data.csv.zip
3,187 test sethttps://github.com/omicscodeathon/denguedrug/blob/main/data/Test Data.csv
3,188 externally-held sethttps://github.com/omicscodeathon/denguedrug/blob/main/data/External Data.csv
https://github.com/omicscodeathon/denguedrug/blob/main/figures/Correlation%20between%20actives%20and%20inactives%20from%20ML_legend.jpeg
https://github.com/omicscodeathon/denguedrug#model-development-and-evaluation
modelshttps://github.com/omicscodeathon/denguedrug/blob/main/output/models
Logistic Regressionhttps://github.com/omicscodeathon/denguedrug/blob/main/output/Models/LR_model.pkl
Table 1https://github.com/omicscodeathon/denguedrug#table-1
https://github.com/omicscodeathon/denguedrug/blob/main/figures/ML_Val_Results.jpeg
https://github.com/omicscodeathon/denguedrug#prediction-of-inhibitors-and-new-compounds
Table 2https://github.com/omicscodeathon/denguedrug#table-2
LR modelhttps://github.com/omicscodeathon/denguedrug/blob/main/output/Models/LR_model.pkl
933https://github.com/omicscodeathon/denguedrug/blob/main/output/ML output
Salgado et al., 2012https://doi.org/10.1097/INF.0b013e3182575e6a
Carocci et al., 2015https://doi.org/10.1128/AAC.04177-14
Fraser et al., 2014https://doi.org/10.1093/infdis/jiu319
Simanjuntak et al., 2015https://doi.org/10.1093/infdis/jiu377
Nguyen et al., 2013https://doi.org/10.1093/infdis/jis470
Ci et al., 2023https://doi.org/10.1016/j.chembiol.2022.10.003
Wu et al., 2011https://doi.org/10.1007/s10875-011-9578-7
Smith et al., 2014https://doi.org/10.1128/JVI.00365-14
Tian et al., 2018https://doi.org/10.1248/cpb.c17-00794
Franco et al., 2021https://doi.org/10.3390/v13050771
Lee et al., 2015https://doi.org/10.1016/j.antiviral.2015.01.002
Lai et al., 2017https://doi.org/https://doi.org/10.1016/j.bcp.2017.01.005
Lai et al., 2017https://doi.org/https://doi.org/10.1016/j.bcp.2017.01.005
de Wispelaere et al., 2013https://doi.org/10.1128/JVI.00632-13
Whitehorn et al., 2016https://doi.org/10.1093/cid/civ949
Byrd et al., 2013https://doi.org/10.1128/AAC.01429-12
Kularatne et al., 2009https://doi.org/10.1136/pgmj.2008.078444
Lai et al., 2017https://doi.org/https://doi.org/10.1016/j.bcp.2017.01.005
Xu et al., 2018https://doi.org/10.1371/journal.pntd.0006934
https://github.com/omicscodeathon/denguedrug#target-selection-and-molecular-docking-of-predicted-compounds
NS2B/NS3 proteasehttps://doi.org/10.3389/fcimb.2023.1061937
Protein Data Bankhttps://www.rcsb.org/
Figure 3https://github.com/omicscodeathon/denguedrug#figure-3
https://github.com/omicscodeathon/denguedrug/blob/main/figures/NS2BNS3 protease structure.png
total ML outputshttps://github.com/omicscodeathon/denguedrug/blob/main/output/ML%20output
Autodock Vinahttps://doi.org/10.1002/jcc.21334
binding affinitieshttps://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular%20Docking/ranked_output.tab
59 compoundshttps://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular%20Docking/Supplemental%201%20-%20Binding%20energies%20and%20intermolecular%20interactions%20between%20compounds%20and%20NS2B_NS3%20protease.csv
Kwofie et al., 2022https://doi.org/10.1002/cbdv.202200160
PyMOLhttps://www.semanticscholar.org/paper/The-PyMOL-Molecular-Graphics-System-(2002)-Delano/9b7284d0e5dfa654db0d97616fa19f371726f9c9
herehttps://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular%20Docking/ranked_output.tab
https://github.com/omicscodeathon/denguedrug#mechanism-of-binding-characterization-of-selected-compounds
LigPlothttps://doi.org/10.1002/jcc.21334
Table 3https://github.com/omicscodeathon/denguedrug#table-3
Supplementary file 1https://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular%20Docking/Supplemental%201%20-%20Binding%20energies%20and%20intermolecular%20interactions%20between%20compounds%20and%20NS2B_NS3%20protease.csv
Table 3https://github.com/omicscodeathon/denguedrug#table-3
Supplementary file 1https://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular%20Docking/Supplemental%201%20-%20Binding%20energies%20and%20intermolecular%20interactions%20between%20compounds%20and%20NS2B_NS3%20protease.csv
Figure 4https://github.com/omicscodeathon/denguedrug#figure-4
https://github.com/omicscodeathon/denguedrug/blob/main/figures/ZIN38628344 protein-ligand interaction_legend.png
PyMOLhttps://www.semanticscholar.org/paper/The-PyMOL-Molecular-Graphics-System-(2002)-Delano/9b7284d0e5dfa654db0d97616fa19f371726f9c9
LigPlothttps://doi.org/10.1021/ci200227u
https://github.com/omicscodeathon/denguedrug#admet-screening-of-selected-compounds
Supplementary Table 2https://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular Docking/Supplemental 2 - ADME Prediction of selected hits and known inhibitors for Pharmacokinetics and Physicochemical profiles.csv
Supplementary Table 2https://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular Docking/Supplemental 2 - ADME Prediction of selected hits and known inhibitors for Pharmacokinetics and Physicochemical profiles.csv
Supplementary Table 2https://github.com/omicscodeathon/denguedrug/blob/main/output/Molecular Docking/Supplemental 2 - ADME Prediction of selected hits and known inhibitors for Pharmacokinetics and Physicochemical profiles.csv
DataWarriorhttps://openmolecules.org/datawarrior/
Table 4https://github.com/omicscodeathon/denguedrug#table-4
https://github.com/omicscodeathon/denguedrug#molecular-dynamics-simulations
GROMACS 2020.5https://doi.org/10.1021/ci500020m
Xmgracehttps://plasma-gate.weizmann.ac.il/Grace/
https://github.com/omicscodeathon/denguedrug#root-mean-square-deviation-rmsd-for-100-ns-md-simulations
Figure 5https://github.com/omicscodeathon/denguedrug#figure-5
https://github.com/omicscodeathon/denguedrug/blob/main/figures/RMSD for NS2B_NS3pro-ligand MD simulations.png
https://github.com/omicscodeathon/denguedrug#radius-of-gyration-for-100-ns-md-simulations
Figure 6https://github.com/omicscodeathon/denguedrug#figure-6
https://github.com/omicscodeathon/denguedrug/blob/main/figures/Rg vs time for NS2B_NS3pro-ligand MD simulations.png
https://github.com/omicscodeathon/denguedrug#root-mean-square-fluctuations-rmsf-for-100-ns-md-simulations
RMSF plothttps://github.com/omicscodeathon/denguedrug#figure-7
RMSF graphhttps://github.com/omicscodeathon/denguedrug#figure-7
https://github.com/omicscodeathon/denguedrug/blob/main/figures/RMSF fluctuations for NS2B_NS3pro-ligand MD simulations.png
https://github.com/omicscodeathon/denguedrug#mmpbsa-computations
https://github.com/omicscodeathon/denguedrug#contributing-energy-terms
Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approachhttps://doi.org/10.1517/17460441.2015.1032936
https://github.com/omicscodeathon/denguedrug#per-residue-energy-decomposition
NS2B/NS3-ZINC14441502 complexhttps://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA%20plot%20of%20binding%20free%20energy%20for%20NS2B_NS3-ZINC14441502.png
Figure 8https://github.com/omicscodeathon/denguedrug#figure-8
NS2B/NS3-ZINC38628344 complexhttps://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA%20plot%20of%20binding%20free%20energy%20for%20NS2B_NS3-ZINC38628344.png
ZINC95485940https://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA%20plot%20of%20binding%20free%20energy%20for%20NS2B_NS3-ZINC95485940.png
2',4'-dihydroxychalconehttps://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA%20plot%20of%20binding%20free%20energy%20for%20NS2B_NS3-2',4'-dihydroxychalcone.png
Prednisolonehttps://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA%20plot%20of%20binding%20free%20energy%20for%20NS2B_NS3-Prednisolone.png
https://github.com/omicscodeathon/denguedrug/blob/main/figures/MMPBSA plot of binding free energy for NS2B_NS3-ZINC14441502.png
https://github.com/omicscodeathon/denguedrug#how-to-use
documentationhttps://github.com/omicscodeathon/denguedrug/blob/main/docs
videoshttps://github.com/omicscodeathon/denguedrug/blob/main/docs/ML_tutorials.txt
pipelinehttps://github.com/omicscodeathon/denguedrug/blob/main/pipeline
Study pipelinehttps://github.com/omicscodeathon/denguedrug/blob/main/pipeline/README.md
https://github.com/omicscodeathon/denguedrug#data-availability
herehttps://github.com/omicscodeathon/denguedrug/blob/main/data
https://github.com/omicscodeathon/denguedrug#reproducibility-prerequisites
Python 3.8https://www.python.org/ftp/python/3.8.0/python-3.8.0-amd64.exe
Anaconda3 2024.06.1https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Windows-x86_64.exe
R 4.3.0https://cran.r-project.org/bin/windows/base/old/4.3.0/R-4.3.0-win.exe
https://github.com/omicscodeathon/denguedrug#credits
0009-0007-2720-9102https://orcid.org/0009-0007-2720-9102
0009-0003-3871-1369https://orcid.org/0009-0003-3871-1369
0009-0004-6104-184Xhttps://orcid.org/0009-0004-6104-184X
0009-0009-1484-4814https://orcid.org/0009-0009-1484-4814
0009-0005-9663-7843https://orcid.org/0009-0005-9663-7843
0009-0009-3419-0483https://orcid.org/0009-0009-3419-0483
0009-0004-9564-6628https://orcid.org/0009-0004-9564-6628
0009-0004-4798-899Xhttps://orcid.org/0009-0004-4798-899X
0000-0002-4257-3611https://orcid.org/0000-0002-4257-3611
Readme https://github.com/omicscodeathon/denguedrug#readme-ov-file
MIT license https://github.com/omicscodeathon/denguedrug#MIT-1-ov-file
Please reload this pagehttps://github.com/omicscodeathon/denguedrug
Activityhttps://github.com/omicscodeathon/denguedrug/activity
Custom propertieshttps://github.com/omicscodeathon/denguedrug/custom-properties
1 forkhttps://github.com/omicscodeathon/denguedrug/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fomicscodeathon%2Fdenguedrug&report=omicscodeathon+%28user%29
Releases 1https://github.com/omicscodeathon/denguedrug/releases
DengueDrug Initial development Latest Jul 11, 2024 https://github.com/omicscodeathon/denguedrug/releases/tag/v0.0.1-alpha
Packages 0https://github.com/orgs/omicscodeathon/packages?repo_name=denguedrug
Please reload this pagehttps://github.com/omicscodeathon/denguedrug
Contributorshttps://github.com/omicscodeathon/denguedrug/graphs/contributors
Please reload this pagehttps://github.com/omicscodeathon/denguedrug
Jupyter Notebook 98.9% https://github.com/omicscodeathon/denguedrug/search?l=jupyter-notebook
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

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