De Novo Drug Design Algorithms
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Comment: Can you check that this topic isn't already covered in one of the articles listed at De novo? DoubleGrazing (talk) 10:12, 10 January 2025 (UTC)
- Comment: Sources 1, 3 and 4 are all cited as if they're the same source, yet all point to different papers (and none is dated 1975); please correct the citations.Also, where is the information in the 'List of Algorithms' section coming from? DoubleGrazing (talk) 10:11, 10 January 2025 (UTC)
Dear DoubleGrazing, sorry for wasting your time. It was my fault for not actually checking the article metadata. The DOI was actually correct for all the articles, I had used the template importer but apparently it does not work on short DOIs. I have now used the correct articles and checked that the metadata is in fact correct. I have checked those De Novo pages, none of them covers de novo small molecule design and as such none of them overlaps with this topic. It would make sense to list this page into that one. Moreover, this is meant to be more of a specialized page rather than a "De Novo Drug Design" page which may be a bit more oriented towards the general public. All the information in 'List of Algorithms' is coming directly from wikidata. I do not know if this is the best approach, my idea is to later use wikidata to connect other relevant information such as code repository for those algorithms. The list is not complete, but I have the intention to gradually add entries throughout the following months. I did not add any source for those algorithms as the DOI is inside the table, and that references the original publication where the algorithm was presented. I assume anybody reading such a technical page should know how to find an article by searching it by DOI. I added a human friendly name for each algorithm, it is either the name given to the algorithm in the paper or the surnames of first and last author. Also, if you know more than me regarding wikidata, could you provide guidance about how I could connect information about the algorithm/software itself to those publication entries or direct me to someone who may know how to do it? Thank you Davidoskky (talk) 21:03, 10 January 2025 (UTC)
De novo drug design is a specialized approach within drug discovery, focusing on the creation of molecular structures with drug-like properties that are distinct from existing therapeutic agents. Unlike traditional drug development, which iteratively modifies known molecules, de novo methods generate novel structures from scratch, leveraging either rational or random approaches. [1] [2] [3]
This technique often utilizes detailed information about the target structure and known binders to generate new patterns of binding.[4]
List of Algorithms
The table below provides a list of algorithms designed for de novo drug design.
| Article Name | DOI | Publication Date |
|---|---|---|
| LigBuilder | 10.1007/S0089400060498 | 2000-08-01 |
| LigBuilder2 | 10.1021/CI100350U | 2011-05-03 |
| LigBuilder3 | 10.3389/FCHEM.2020.00142 | 2020-02-28 |
| Popova-Tropsha | 10.1126/SCIADV.AAP7885 | 2018-07 |
| LigDream | 10.1021/ACS.JCIM.8B00706 | 2019-02-28 |
| MEGA | 10.1186/1752-153X-3-S1-P22 | 2009 |
| GroupBuild | 10.1021/JM00064A003 | 1993-06-01 |
| Li-Liu | 10.1186/S13321-018-0287-6 | 2018-07-24 |
| MoGADdrug | 10.2174/1573409916666200620194143 | 2020-06-20 |
| Polykovskiy-Kadurin | 10.1021/ACS.MOLPHARMACEUT.8B00839 | 2018-09-19 |
| Ligand | 10.1063/1.47765 | 1995 |
| DeepScaffold | 10.1021/ACS.JCIM.9B00727 | 2019-12-20 |
| reinvent-scaffold-decorator | 10.26434/CHEMRXIV.11638383 | 2020-01-21 |
| GenStar | 10.1007/BF00141573 | 1993-02-01 |
| REINVENT 2.0 | 10.1021/ACS.JCIM.0C00915 | 2020-10-29 |
| Masek | 10.1021/ACS.JCIM.5B00697 | 2016-03-31 |
| moo-denovo | 10.1021/ACS.JCIM.0C00517 | 2020-08-26 |
See also
References
- ^ Moon, Joseph B.; Howe, W.Jeffrey (January 1990). "3D database searching and de novo construction methods in molecular design". Tetrahedron Computer Methodology. 3 (6): 697–711. doi:10.1016/0898-5529(90)90168-8.
- ^ Martinelli, Dominic D. (June 2022). "Generative machine learning for de novo drug discovery: A systematic review". Computers in Biology and Medicine. 145: 105403. doi:10.1016/j.compbiomed.2022.105403.
- ^ Crucitti, Davide; Pérez Míguez, Carlos; Díaz Arias, José Ángel; Fernandez Prada, Diego Beltrán; Mosquera Orgueira, Adrián (25 January 2024). "De novo drug design through artificial intelligence: an introduction". Frontiers in Hematology. 3. doi:10.3389/frhem.2024.1305741.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Tang, Yidan; Moretti, Rocco; Meiler, Jens (25 March 2024). "Recent Advances in Automated Structure-Based De Novo Drug Design". Journal of Chemical Information and Modeling. 64 (6): 1794–1805. doi:10.1021/acs.jcim.4c00247.