{ "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/2025/03/11/CDK-UGM.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/e08pe-thb38", "url": "https://chem-bla-ics.linkedchemistry.info/2025/03/11/CDK-UGM.html", "title": "cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1", "content_html": "

As part of our Dutch Research Council (NWO) Open Science grant,\nwe organized a Chemistry Development Kit User Group Meeting\n(#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon.

\n\n

I opened the session with a few slides welcoming everyone at Maastricht University (and our\nDept of Translational Genomics,\nand explaining the NWO grant.\nJohn Mayfield (NextMove) spoke about\n“What’s New” in the Chemistry Development Kit 2.10, e.g. explaining more about the new (much faster) AtomContainer,\nSMIRKS, and more.

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After lunch, Jonas Schaub (Friedrich Schiller University Jena)\nshowed various projects where the CDK is used, titled “Scaffolds, Functional Groups, Aglycones: Algorithmic Substructure Identification with CDK”\n(see doi:10.1186/s13321-023-00762-4, doi:10.1186/s13321-022-00656-x,\nand doi:10.1186/s13321-020-00467-y).\nLyudvika Radeva (Ideaconsult Ltd, University of Plovdiv) showed\nwhat SYBYL Line Notation (SLN) is and how this is implemented in Ambit (see doi:10.1002/minf.202100027).\nSonja Herres-Pawlis (RWTH Aachen University)\nupdated us with “News from the InChI: making the InChI FAIR and including inorganics”, e.g. showing how\nthey worked out how the InChI is going to handle organometalics, where the bonds and the stereochemistry\nas aspects that were not handled by the current InChI.

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After the afternoon coffee break, Zhixu Ni (TU Dresden)\nshowed his work on lipid maps characterization and identification. We previously met a few times\nat EpiLipidNET COST action meetings, and it was great to see his continued research on representation\nof lipids and lipid classes in hit “A Fuzzy Solution for Lipid Structures Using CXSMILES”.

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Finally, Matthias Mailänder (Lablicate GmbH)\ngave a “Live demo of where OpenChrom uses the CDK”, and\nYajie Ding (University of Groningen) told her about her\nglycoscience research. There, cheminformatics can also greatly help and the CDK may provide\nthem with solutions.

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This really doesn’t do justice to all the discussions, examples, use cases, etc. But it gives you\nan idea. We had 11 people in the room, and were joined online by an additional 6 people.

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References

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Chandrasekhar, V., Sharma, N., Schaub, J., Steinbeck, C., & Rajan, K. (2023). Cheminformatics Microservice: unifying access to open cheminformatics toolkits. Journal of Cheminformatics, 15(1). https://doi.org/10.1186/s13321-023-00762-4 CrossRef Scholia
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Kochev, N., Jeliazkova, N., & Tancheva, G. (2021). Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation. Molecular Informatics, 40(11). https://doi.org/10.1002/minf.202100027 CrossRef Scholia
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Schaub, J., Zander, J., Zielesny, A., & Steinbeck, C. (2022). Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). Journal of Cheminformatics, 14(1). https://doi.org/10.1186/s13321-022-00656-x CrossRef Scholia
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Schaub, J., Zielesny, A., Steinbeck, C., & Sorokina, M. (2020). Too sweet: cheminformatics for deglycosylation in natural products. Journal of Cheminformatics, 12(1). https://doi.org/10.1186/s13321-020-00467-y CrossRef Scholia
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", "summary": "As part of our Dutch Research Council (NWO) Open Science grant, we organized a Chemistry Development Kit User Group Meeting (#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon.", "date_published": "2025-03-11T00:00:00+00:00", "date_modified": "2025-03-11T14:00:00+00:00", "tags": ["cdk","openscience","cdk2024"], "_references": [ { "url": "https://doi.org/10.1002/minf.202100027", "doi": "10.1002/minf.202100027" } , { "url": "https://doi.org/10.1186/s13321-022-00656-x", "doi": "10.1186/s13321-022-00656-x" } , { "url": "https://doi.org/10.1186/s13321-023-00762-4", "doi": "10.1186/s13321-023-00762-4" } , { "url": "https://doi.org/10.1186/s13321-020-00467-y", "doi": "10.1186/s13321-020-00467-y" } ], "_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" } ] } ] }