Wikipedia:Articles for deletion/LeDock

The following discussion is an archived debate of the proposed deletion of the article below. Please do not modify it. Subsequent comments should be made on the appropriate discussion page (such as the article's talk page or in a deletion review). No further edits should be made to this page.

The result was no consensus‎. I don't see a consensus here. Liz ^{Read! Talk!} 02:20, 29 August 2023 (UTC)[reply]

LeDock

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Does not appear to meet WP:NPRODUCT - tagged as such, and digging into the sources included, one is an unencyclopedic source, two are from one author, and five are from another author. The original article appears to be from a WP:SPA, and the article reads a bit like an advert. Courtesy ping Bbb23 as they declined the speedy for G11. In fact, I am not finding mentions in half of the listed sources. Tried searching more on Google scholar and found only one other top ranked source that contained this topic and that top result is just a trivial mention. Aasim - Herrscher of Wikis ❄️ 01:10, 8 August 2023 (UTC)[reply]

Weak Delete Found an article [1] about the software, which looks reliable, but possibly not independent. Sources cited in article are mostly passing mentions. Neutral following edits made below. WeirdNAnnoyed (talk) 01:35, 8 August 2023 (UTC)[reply]
Note: This discussion has been included in the list of Software-related deletion discussions. Shellwood (talk) 01:47, 8 August 2023 (UTC)[reply]
Delete unless significant coverage in entirely independent sources can be found. Journal articles written by the developers are not independent. Cullen328 (talk) 01:56, 8 August 2023 (UTC)[reply]
Note: This discussion has been included in the deletion sorting lists for the following topics: Biology, Medicine, and Science. --A. B. ^{(talk • contribs • global count)} 03:46, 8 August 2023 (UTC)[reply]

Notifications left at Wikipedia talk:WikiProject Pharmacology, Wikipedia talk:WikiProject Molecular Biology/Computational Biology, and Wikipedia talk:WikiProject Molecular Biology. --A. B. ^{(talk • contribs • global count)} 03:58, 8 August 2023 (UTC)[reply]
First off, I want to say that it is especially weird that a piece of software like this, coming out of an academic lab, does not have the primary citation listed at its website clearly. Further, that primary citation does not even use the software's name. I had to pull it from the Wang et al 2016 publication. Reference 1 (Wang et al 2016) does qualify as significant coverage in an independent source. This paper published a couple weeks ago is similar to the 2016 article in that it compares docking programs for a specific application. Both are technically primary sources I guess, but are essentially software reviews/benchmarking. Searching the scholar results for secondary sources that cite the main LeDock publication finds passing mentions in other review articles, especially just referring to the Wang et al 2016 results, for example, [2] and [3]. The second does not even mention LeDock by name. There are more review articles that cite the main publication, but I didn't see anything that wasn't more than a passing mention.

Neutral on whether this gets deleted or not. There's definitely value in the software and more could be written about it, but the article here is lacking. This is a niche corner of biochemistry, and I don't think people should be surprised if there is no Wikipedia article about a particular piece of software used in it. For reference LeDock isn't as popular as other docking software. LeDock is cited ~100 times DOCK6 is cited ~800 times and AutoDock VINA is cited ~25000 times. ― Synpath 06:43, 8 August 2023 (UTC)[reply]

Delete This is an article that’s of little interest to anyone who doesn’t already know about this software. We don’t need to clutter up Wikipedia with stuff like this. Genome42 (talk) 09:21, 8 August 2023 (UTC)[reply]
Delete Per rationale by Cullen. Jamiebuba (talk) 19:39, 8 August 2023 (UTC)[reply]

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Extra sources:

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. Bibcode:2019E&ES..218a2143L. doi:10.1088/1755-1315/218/1/012143. ISSN 1755-1315. S2CID 86585788.

"Applications of LeDock Software - CD ComputaBio". CD ComputaBio. Retrieved 2023-08-08.

Moreno, Angel J. Ruiz (2021-09-18). "Molecular Docking". Cheminformatics Workflows. Retrieved 2023-08-08.

Kamal, Izaz Monir; Chakrabarti, Saikat (2023-02-14). "MetaDOCK: A Combinatorial Molecular Docking Approach". ACS Omega. 8 (6): 5850–5860. doi:10.1021/acsomega.2c07619. ISSN 2470-1343. PMC 9933224. PMID 36816658.5850-5860&rft.date=2023-02-14&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933224#id-name=PMC&rft.issn=2470-1343&rft_id=info:pmid/36816658&rft_id=info:doi/10.1021/acsomega.2c07619&rft.aulast=Kamal&rft.aufirst=Izaz Monir&rft.au=Chakrabarti, Saikat&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933224&rfr_id=info:sid/en.wikipedia.org:Wikipedia:Articles for deletion/LeDock" class="Z3988">

Fan, Jiyu; Fu, Ailing; Zhang, Le (2019). "Progress in molecular docking". Quantitative Biology. 7 (2): 83–89. doi:10.1007/s40484-019-0172-y. ISSN 2095-4689. S2CID 164411377.83-89&rft.date=2019&rft_id=https://api.semanticscholar.org/CorpusID:164411377#id-name=S2CID&rft.issn=2095-4689&rft_id=info:doi/10.1007/s40484-019-0172-y&rft.aulast=Fan&rft.aufirst=Jiyu&rft.au=Fu, Ailing&rft.au=Zhang, Le&rft_id=https://journal.hep.com.cn/qb/EN/10.1007/s40484-019-0172-y&rfr_id=info:sid/en.wikipedia.org:Wikipedia:Articles for deletion/LeDock" class="Z3988">

Bai, Qifeng; Liu, Shuo; Tian, Yanan; Xu, Tingyang; Banegas‐Luna, Antonio Jesús; Pérez‐Sánchez, Horacio; Huang, Junzhou; Liu, Huanxiang; Yao, Xiaojun (2022). "Application advances of deep learning methods for de novo drug design and molecular dynamics simulation". WIREs Computational Molecular Science. 12 (3). doi:10.1002/wcms.1581. ISSN 1759-0876. S2CID 244580270.

Chen, Fangling; Wang, Zhuoya; Wang, Chaoyi; Xu, Qingliang; Liang, Jiazhen; Xu, Ximing; Yang, Jinbo; Wang, Changyun; Jiang, Tao; Yu, Rilei (2017). "Application of reverse docking for target prediction of marine compounds with anti-tumor activity". Journal of Molecular Graphics and Modelling. 77: 372–377. doi:10.1016/j.jmgm.2017.09.015. PMID 28950183.372-377&rft.date=2017&rft_id=info:doi/10.1016/j.jmgm.2017.09.015&rft_id=info:pmid/28950183&rft.aulast=Chen&rft.aufirst=Fangling&rft.au=Wang, Zhuoya&rft.au=Wang, Chaoyi&rft.au=Xu, Qingliang&rft.au=Liang, Jiazhen&rft.au=Xu, Ximing&rft.au=Yang, Jinbo&rft.au=Wang, Changyun&rft.au=Jiang, Tao&rft.au=Yu, Rilei&rft_id=https://linkinghub.elsevier.com/retrieve/pii/S1093326317305879&rfr_id=info:sid/en.wikipedia.org:Wikipedia:Articles for deletion/LeDock" class="Z3988">

Dhananjayan, Karthik (2015-03-22). "Molecular Docking Study Characterization of Rare Flavonoids at the Nac-Binding Site of the First Bromodomain of BRD4 (BRD4 BD1)". Journal of Cancer Research. 2015: 1–15. doi:10.1155/2015/762716. ISSN 2356-7201.1-15&rft.date=2015-03-22&rft_id=info:doi/10.1155/2015/762716&rft.issn=2356-7201&rft.aulast=Dhananjayan&rft.aufirst=Karthik&rft_id=https://doi.org/10.1155%2F2015%2F762716&rfr_id=info:sid/en.wikipedia.org:Wikipedia:Articles for deletion/LeDock" class="Z3988">

Zheng, Liangzhen; Meng, Jintao; Jiang, Kai; Lan, Haidong; Wang, Zechen; Lin, Mingzhi; Li, Weifeng; Guo, Hongwei; Wei, Yanjie; Mu, Yuguang (2022-05-13). "Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term". Briefings in Bioinformatics. 23 (3). doi:10.1093/bib/bbac051. ISSN 1467-5463. PMC 9116214. PMID 35289359.

— Arthurfragoso (talk) 19:47, 8 August 2023 (UTC)[reply]

~~Weak keep~~ - I usually don't find enough biochemical software that works on Linux. I did not have a previous knowledge about this LeDock software, it seems it is mostly used in China. And I hope we don't get a western bias in the way of this decision. I have to think more before I give a "neutral" or "keep" vote. — Arthurfragoso (talk) 20:08, 8 August 2023 (UTC)[reply]

I just have put some work on improving the article. -- Arthurfragoso (talk) 18:55, 9 August 2023 (UTC)[reply]

keep - I've made additional modifications and included a Nature article that conducted benchmarks on it. Perhaps those who previously voted for deletion could reconsider and re-evaluate. — Arthurfragoso (talk) 20:41, 9 August 2023 (UTC)[reply]

Have you assessed the WP:RELIABILITY? That Nature article appears to be a lab report which is a WP:PRIMARY source. If there is a WP:SECONDARY source that takes an aggregate of these studies and reports and gives nontrivial coverage that would be amazing :) Aasim - Herrscher of Wikis ❄️ 23:06, 9 August 2023 (UTC)[reply]

If this were an article or statement about a disease or treatment, a journal article like this Nature piece would be a primary source. However, for software, maybe the primary source is the material coming directly from the company, like the website. So in this case, I think, the Nature article is considered a secondary source, while a meta-analysis would be a tertiary source. About the reliability, I did not really like the Baidu source I added, as their captcha prevents archiving it in the waybackmachine. -- Arthurfragoso (talk) 03:04, 10 August 2023 (UTC)[reply]

Relisted to generate a more thorough discussion and clearer consensus.
Relisting comment: Relisting in light of the new sources brought up. Do they change any minds of those advocating Deletion?
Please add new comments below this notice. Thanks, Liz ^{Read! Talk!} 01:27, 15 August 2023 (UTC)[reply]

Keep It's a peer-reviewed Primary source if that makes sense; the author of the paper/creator of the software submitted the paper to the journal for validation, it was accepted and published in the journal. It's been validated by the journal staff as being correct, so it's a RS. Oaktree b (talk) 01:51, 15 August 2023 (UTC)[reply]

I think we're getting too far down into the weeds on this; it's sourced to peer-reviewed journals, not blog posts. I surmise the article is fine with what's given for sources. Oaktree b (talk) 01:52, 15 August 2023 (UTC)[reply]

Relisted to generate a more thorough discussion and clearer consensus.
Please add new comments below this notice. Thanks, Liz ^{Read! Talk!} 03:44, 22 August 2023 (UTC)[reply]

Keep: Per arguments and sources presented by Arthurfragoso and Oaktree b.CarribeanKing (talk) 20:09, 22 August 2023 (UTC)[reply]

The above discussion is preserved as an archive of the debate. Please do not modify it. Subsequent comments should be made on the appropriate discussion page (such as the article's talk page or in a deletion review). No further edits should be made to this page.