Prachi Srivastava Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India
Saurabh Kumar Student, Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh,, India
Shraddha Pandey Student, Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh,, India
Shrijal Singh Student, Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India
Address for correspondence: Prachi Srivastava, Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India E-mail: psrivastava@amity.edu
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Saurabh Kumar, Shraddha Pandey, Shrijal Singh, Prachi Srivastava. Insight of Computational Tools, Software
and Databases in CADD. International Journal of Neurology and Neurosurgery. 2025; 17(2): 116-123.
Timeline
Received : March 13, 2025
Accepted : May 08, 2025
Published : July 30, 2025
Abstract
Considering the emergence of several different computational tools, databases and software the process of drug study and development has become substantially easier. The novel development of drugs method is transformed by computer- aided drug design because it is rapid, economically viable, and efficient in terms of time and it has higher levels of pharmacological activity. It includes molecular docking, molecular dynamic simulations, quantitative structure activity relationship (QSAR) modelling. Uses several software platforms for virtual screening, lead optimization, designing novel chemotypes, emphasizes its application in rational
drug design. It also underscores the significance that specialized databases are for supplying vital information for drug development, such chemical libraries, protein target repositories, Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) databases.
References
1. Niazi, S.K., & Mariam, Z. (2024). ComputerAided Drug Design and Drug Discovery: A Prospective Analysis. Pharmaceuticals, 17(1), 22.
2. Soma Mandal, Mee’nal Moudgil, Sanat K. Mandal, Rational drug design, European Journal of Pharmacology, Volume 625, Issues 1–3, 2009, Pages 90-100, ISSN 0014-2999.
3. Batool, M., Ahmad, B., & Choi, S. (2019). A Structure-Based Drug Discovery Paradigm. International Journal of Molecular Sciences, 20(11), 2783. https://doi.org/10.3390/ ijms20112783
4. Prajapat, P., Agarwal, S., &Talesara, G. L. (2017). Significance of computer aided drug design and 3D QSAR in modern drug discovery. J Med Org Chem, 1(1), 1.
5. Vivek Yadav, Jurnal Reang, Vinita, Rajiv Kumar Tonk, Chapter 3 - Ligand-based drug design (LBDD), Editor(s): Mithun Rudrapal, ChukwuebukaEgbuna, In Drug Discovery Update, Computer Aided Drug Design (CADD): From Ligand-Based Methods to Structure-Based Approaches, Elsevier, 2022, Pages 57-99, ISBN 9780323906081
6. Hemant Arya, Mohane Selvaraj Coumar, Chapter 4 - Lead identification and optimization, Editor(s): Tarun Kumar Bhatt, Surendra Nimesh, The Design & Development
7. Temitope Isaac Adelusi, Abdul-Quddus Kehinde Oyedele, Ibrahim DamilareBoyenle, Abdeen Tunde Ogunlana, RofiatOluwabusola Adeyemi, Chiamaka Divine Ukachi, Mukhtar Oluwaseun Idris, Olamide Tosin Olaoba, Ibrahim OlaideAdedotun, Oladipo Elijah Kolawole, Yin Xiaoxing, Misbaudeen AbdulHammed, Molecular modeling in drug discovery, Informatics in Medicine Unlocked, Volume 29, 2022, 100880, ISSN 2352-9148
8. Keil, Matthias & Marhoefer, Richard & Rohwer, Andreas & Selzer, Paul & Brickmann, Jurgen & Korb, Oliver & Exner, Thomas. (2009). Molecular visualization in the rational drug design process. Frontiers in bioscience: a journal and virtual library. 14. 2559-83. 10.2741/3398.
9. Tulloch L.B., Menzies S.K., Coron R.P., Roberts M.D., Florence G.J., Smith T.K. Direct and indirect approaches to identify drug modes of action. IUBMB Life. 2018 Jan; 70(1): 9-22. doi: 10.1002/iub.1697. Epub 2017 Dec 6. PMID: 29210173.
10. Ashish A. Gawai, Kailash R. Biyani, Sanjib Das, Ganesh G. Tapadiya, Santosh N. Mokale, Sachin A. Dhawale, Design, Synthesis, Molecular Docking, and Preliminary Pharmacological Screening of some New Benzodthiazol-2-ylamino Containing Chromen-2- one Derivatives with Atypical Antipsychotic Profile, Current ComputerAided Drug Design, 10.2174/157340991966623 0202105207, 19, 6, (465-475), (2023).
11. Hanwell, M.D., Curtis, D.E., Lonie, D.C. et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4, 17 (2012).
12. Schrodinger Molecular Modelling Suite – DUCC. ducc.du.ac.in/wp3/schrodingermolecular-modelling-suit.
13. Sanne Abeln, Klaas Anton Feenstra, Jaap Heringa, Protein Three-Dimensional Structure Prediction, Editor(s): Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach, Encyclopedia of Bioinformatics and Computational Biology, Academic Press, 2019, Pages 497-511, ISBN 9780128114322
14. Li H., Wei X. A Concise Review of Biomolecule Visualization. Curr Issues Mol Biol. 2024 Feb 2; 46(2): 1318-1334. doi: 10.3390/cimb46020084.
15. Iqbal, Muhammad & Shahab, Muhammad & Zheng, Guojun& Sun, Xinxiao& Yuan, Qipeng. (2025). 41598 2024 Article 78232. doi.org/10.3390/ijms20184574
17. Henrik Land, Maria Svedendahl Humble Series: Methods In Molecular Biology >, Book: Protein Engineering Protocol | DOI: 10.1007/978-1-4939-7366-8_4
18. Torres, P.H.M., Sodero, A.C.R., Jofily, P., & Silva-Jr, F.P. (2019). Key Topics in Molecular Docking for Drug Design. International journal of molecular sciences, 20(18), 4574. https://
19. Agu, P.C., Afiukwa, C.A., Orji, O.U. et al. Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management. Sci Rep 13, 13398 (2023).
21. Super User. “Detailed Comparison: Gromacs vs. Amber for Molecular Dynamics Simulations.” Parssilico.com, 2025, parssilico.com/blogs/85- gromacs-vs-amber-md-software. Accessed 1 Feb. 2025.
22. Pratibha Chaurasia, Anasuya Bhargav, Srinivasan Ramachandran, Chapter 28 – Free tools and databases in ligand and structurebased drug design, Editor(s): Kunal Roy, Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development, Academic Press, 2023, Pages
23. Verma, J., Khedkar, V.M., & Coutinho, E.C. (2010). 3D-QSAR in drug design-a review. Current topics in medicinal chemistry, 10(1), 95-115.
24. Oliveira TAd, Silva MPd, Maia EHB, Silva AMd, Taranto AG. Virtual Screening Algorithms in Drug Discovery: A Review Focused on Machine and Deep Learning Methods. Drugs and Drug Candidates. 2023; 2(2):311-334.
25. Hemant Arya, Mohane Selvaraj Coumar, Chapter 4 - Lead identification and optimization, Editor(s): Tarun Kumar Bhatt, Surendra Nimesh, The Design & Development of Novel Drugs and Vaccines, Academic Press, 2021, Pages 31-63, ISBN 9780128214718
26. author = “J. Bienstock, Rachelle”, title = “Computational Drug Design Targeting Protein-Protein Interactions”, journal= “Current Pharmaceutical Design”, year = “2012”, volume = “18”, number = “9”, pages = “1240-1254”, doi = “https://doi.org/10.2174 /138920012799362891”, publisher = “Bentham Science Publishers”, issn = “1873-4286”, type = “Journal Article”
27. Dong Zou, Lina Ma, Jun Yu, Zhang Zhang, Biological Databases for Human Research, Genomics, Proteomics & Bioinformatics, Volume 13, Issue 1, 2015, Pages 55-63, ISSN 1672-0229.
28. Paolini G.V., Shapland R.H.B., van Hoorn W.P., Mason J.S., Hopkins A.L. Global mapping of pharmacological space. Nat. Biotechnol. 2006; 24: 805–815. doi: 10.1038/nbt1228
29. David S. Wishart, Yannick D. Feunang, An C. Guo, Elvis J. Lo, Ana Marcu, Jason R. Grant, Tanvir Sajed, Daniel Johnson, Carin Li, ZinatSayeeda, Nazanin Assempour, IthayavaniIynkkaran, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, Michael Wilson, DrugBank 5.0: a major update to the DrugBank database for 2018, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D1074–D1082
30. Bassani, D., & Moro, S. (2023). Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies. Molecules, 28(9),3906. https://doi.org/10.3390/molecules28093906
31. Baig, M.H., Ahmad, K., Rabbani, G., Danishuddin, M., & Choi, I. (2018). Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders. Current
Data Sharing Statement
There are no additional data available. All raw data and code are available upon request.
Funding
This research received no funding.
Author Contributions
All authors contributed significantly to the work and approve its publication.
Ethics Declaration
This article does not involve any human or animal subjects, and therefore does not require ethics approval.
Acknowledgements
We would like to express our gratitude to the patients, their families, and all those who have contributed to this study.
Conflicts of Interest
No conflicts of interest in this work.
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Cite this article
Saurabh Kumar, Shraddha Pandey, Shrijal Singh, Prachi Srivastava. Insight of Computational Tools, Software
and Databases in CADD. International Journal of Neurology and Neurosurgery. 2025; 17(2): 116-123.
This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.