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Use of Freely Available and Open Source Tools for In Silico Screening in Chemical Biology

https://doi.org/10.1021/ed400302u
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.21256openalex-snapshot
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/minf.200900015openalex-snapshot
Structuring Chemical Space: Similarity‐Based Characterization of the PubChem Database
inferredcites →https://doi.org/10.1006/jmbi.1990.9999openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/j.chembiol.2011.12.012openalex-snapshot
Systems Biology and Systems Chemistry: New Directions for Drug Discovery
inferredcites →https://doi.org/10.1016/j.drudis.2012.10.007openalex-snapshot
Four disruptive strategies for removing drug discovery bottlenecks
inferredcites →https://doi.org/10.1021/ci0496797openalex-snapshot
LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities
inferredcites →https://doi.org/10.1021/ci3001277openalex-snapshot
ZINC: A Free Tool to Discover Chemistry for Biology
inferredcites →https://doi.org/10.1021/ed073p104openalex-snapshot
Computational Chemistry for the Masses
inferredcites →https://doi.org/10.1021/ed100193mopenalex-snapshot
Using the β2-Adrenoceptor for Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/ed200151bopenalex-snapshot
Integrated Teaching of Structure-Based Drug Design and Biopharmaceutics: A Computer-Based Approach
inferredcites →https://doi.org/10.1021/jm9006966openalex-snapshot
Automated Docking Screens: A Feasibility Study
inferredcites →https://doi.org/10.1038/nchembio.118openalex-snapshot
Network pharmacology: the next paradigm in drug discovery
inferredcites →https://doi.org/10.1038/nchembio.926openalex-snapshot
A combinatorial TIR1/AFB–Aux/IAA co-receptor system for differential sensing of auxin
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1109/cibcb.2012.6217214openalex-snapshot
idock: A multithreaded virtual screening tool for flexible ligand docking
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1371/journal.pntd.0000418openalex-snapshot
A Kernel for Open Source Drug Discovery in Tropical Diseases
inferredcites →https://doi.org/10.4155/fmc.11.63openalex-snapshot
Software and Resources for Computational Medicinal Chemistry

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s11030-025-11199-2openalex-snapshot
Machine learning: Python tools for studying biomolecules and drug design
inferred← citeshttps://doi.org/10.1007/s13738-021-02235-7openalex-snapshot
Repositioning therapeutics for COVID-19: virtual screening of the potent synthetic and natural compounds as SARS-CoV-2 3CLpro inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113390openalex-snapshot
Structure-based drug design of an inhibitor of the SARS-CoV-2 (COVID-19) main protease using free software: A tutorial for students and scientists
inferred← citeshttps://doi.org/10.1016/j.sciaf.2025.e03174openalex-snapshot
Computational insights into Croton species as sources of CDK4/6 inhibitors for cancer therapy
inferred← citeshttps://doi.org/10.1021/acs.jchemed.0c01363openalex-snapshot
Potential for Chemistry in Multidisciplinary, Interdisciplinary, and Transdisciplinary Teaching Activities in Higher Education
inferred← citeshttps://doi.org/10.1021/acs.jchemed.1c00289openalex-snapshot
Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master’s Students to Undertake Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jchemed.3c00307openalex-snapshot
Design and Implementation of an Accessible and Open-Sourced In Silico Drug Screening Activity for Cancer Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jchemed.6b00555openalex-snapshot
Demonstration of AutoDock as an Educational Tool for Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jchemed.6b00596openalex-snapshot
Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public
inferred← citeshttps://doi.org/10.1021/acs.jchemed.8b00712openalex-snapshot
Computer-Aided Drug Design for Undergraduates
inferred← citeshttps://doi.org/10.1021/acschembio.7b00986openalex-snapshot
Innovations in Undergraduate Chemical Biology Education
inferred← citeshttps://doi.org/10.1021/acschembio.8b00527openalex-snapshot
The Tetrazole Analogue of the Auxin Indole-3-acetic Acid Binds Preferentially to TIR1 and Not AFB5
inferred← citeshttps://doi.org/10.1021/ed500195dopenalex-snapshot
Using Free Computational Resources To Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course
inferred← citeshttps://doi.org/10.1021/ed5006739openalex-snapshot
Using Internet Databases for Food Science Organic Chemistry Students To Discover Chemical Compound Information
inferred← citeshttps://doi.org/10.1186/s13321-019-0406-zopenalex-snapshot
Learning cheminformatics
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