{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/ytkmr-0vv92", "url": "https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html", "title": "cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit", "content_html": "

We recently got awarded our second \nNWO Open Science grant (OSF23.2.097),\nthis time for the Chemistry Development Kit (CDK).\n“We” here is me and Alyanne de Haan, René van der Ploeg, and\nMarc Teunis from Hogeschool Utrecht.\nThe proposal has been submitted for public dissemination in RIO Journal, like\nwe did \nwith the first NWO Open Science grant.

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The project formally started on April 1 but we had our kick-off meeting in Maastricht on April 4-5.\nWe were joined by Javier and on the second day by Marvin, and Ozan from our BiGCaT research group\nin Maastricht. During this hackathon, I gave a (repeat) presentation\nabout the history of the CDK which also included the problem that software using the CDK does not\nalways use the most recent version.

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And that, upgrading tools using the CDK with the latest CDK version, is the main topic of this grant (work package 2, WP2).\nThe full proposal has the focus list of tools, but most of it is also listed in\nthe issue tracker we have set up as project\nmanagement tool on GitHub.

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Second, we actually hacked together on two first tools, one on our focus list, but the other that was\nrequested we have a look at too: SMARTCyp.\nThe latest version uses RDKit (doi:10.1093/bioinformatics/btz037),\nbut the original version uses the CDK (doi:10.1021/ml100016x).

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We downloaded the source code of SMARTCyp 2.4.2, started taking notes,\nJavier started a Maven build environment, updated a lot of code, but we seem quite close to a version that can be tested by\npeople that have integrated SMARTCyp in other tools. This is based on CDK 2.9\nand if you ignore the 2D depiction glitch, it looks it was a nice first choice:

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On a final note, we plan to record carefully our steps, in an open notebook science approach, with\nthe intention to extract general upgrade steps. For example, we will update the\nMigration section of the\nGroovy Cheminformatics with the Chemistry Development Kit.

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References

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Olsen, L., Montefiori, M., Tran, K. P., & Jørgensen, F. S. (2019). SMARTCyp 3.0: enhanced cytochrome P450 site-of-metabolism prediction server. Bioinformatics, 35(17), 3174–3175. https://doi.org/10.1093/bioinformatics/btz037 CrossRef Scholia
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Rydberg, P., Gloriam, D. E., Zaretzki, J., Breneman, C., & Olsen, L. (2010). SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism. ACS Medicinal Chemistry Letters, 1(3), 96–100. https://doi.org/10.1021/ml100016x CrossRef Scholia
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", "summary": "We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/smartcyp.png", "date_published": "2024-04-07T00:00:00+00:00", "date_modified": "2025-03-11T00:00:00+00:00", "tags": ["grant","cdk","cdk2024"], "_references": [ { "url": "https://doi.org/10.1093/bioinformatics/btz037", "doi": "10.1093/bioinformatics/btz037" } , { "url": "https://doi.org/10.1021/ml100016x", "doi": "10.1021/ml100016x" } ], "_funding": [{"award": { "title" : "The Chemistry Development Kit in 2024: improving cheminformatics research", "acronym" : "CDK2024", "uri" : "drc.filenumber:osf232097" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } }], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }