{ "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/2009/05/11/pubchem-cdk.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/10.59350/8bpsk-rb857", "url": "https://chem-bla-ics.linkedchemistry.info/2009/05/11/pubchem-cdk.html", "title": "PubChem-CDK", "content_html": "

PubChem-CDK is a project that runs CDK code on the PubChem data.\nAs we speak, a groovy script reads about 100 PubChem Compounds XML entries per second into the database. Mind you, not the SDF they distribute which uses a\ncustom extension to overcome the limits of the real MDL SDF format.

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Right now, it has run the atom type perception algorithm on about 1M compounds, and has a pretty good coverage of the organic chemistry domain. I will\nanalyze the results statistically soon, but will likely use this data first to add some missing atom types\nto CDK 1.2.x. BTW, did you know only three carbon atoms failed?\nA C4- (CID:156031), a C3+ (CID:161072),\nand a C2+ (CID:161073). Would your cheminformatics library know what their properties are?

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It is really nice way of browsing PubChem, BTW. For example, did you know there are several boron compounds which have a substructure [N+]-[B+]-[N+]? Yes,\nthree positive charges, next to each other? For example (CID:3612285):

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Well, neither did I. How was it synthesised? What are the spectral properties? How do they stabilise it? What magic counter ion? PubChem, unfortunately,\ndoes not have links to primary literature, and there is no free source for that available. A failure in chemistry. The source points to\nChemDB, but the entry in that database does\nnot shed light on this either.

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Anyway, more on this later. Much more, as I plan to run many CDK algorithms on this code.

", "summary": "PubChem-CDK is a project that runs CDK code on the PubChem data. As we speak, a groovy script reads about 100 PubChem Compounds XML entries per second into the database. Mind you, not the SDF they distribute which uses a custom extension to overcome the limits of the real MDL SDF format.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/CID3612285.png", "date_published": "2009-05-11T00:00:00+00:00", "date_modified": "2009-05-11T00:00:00+00:00", "tags": ["cdk","pubchem"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }