{
  "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/2019/10/09/chemcuration-small-trick-to-fix-smiles.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/preah-ehh72",
      "url": "https://chem-bla-ics.linkedchemistry.info/2019/10/09/chemcuration-small-trick-to-fix-smiles.html",
      "title": "ChemCuration: a small trick to fix the SMILES of glucuronides",
      "content_html": "<p><span style=\"width: 40%; display: block; margin-left: auto; margin-right: auto; float: right\">\n<img src=\"/assets/images/Screenshot_20191008_144049.png\" /> <br />\nGlucuronide functional group.\n</span></p>\n\n<p>Now that the <a href=\"https://chemcuration.github.io/chemcuration2019/\">ChemCuration 2019</a> online poster conference is nearing, and\nmy upcoming talks about chemistry in <a href=\"https://wikidata.org/\">Wikidata</a> (also needing curation), and the much longer process\nof curation of metabolite (-like) structures in <a href=\"https://wikipathways.org/\">WikiPathways</a>, I decided that something I\ntweeted earlier this week is actually quite useful, and therefore something I should really write up in my lab notebook.</p>\n\n<p><a href=\"https://en.wikipedia.org/wiki/Glucuronide\">Glucuronide</a> is an example (biological) functional group. And there are several\ndatabases that represent the stereochemistry now always correct. That is an interoperability (and thus FAIR) problem.\nCorrecting this is not trivial, particularly if you have to redraw the same glucuronide group again and again.</p>\n\n<p>So, not looking forward to that, I invested a bit of time to find a <a href=\"http://opensmiles.org/\">SMILES</a> trick. What if I had\na SMILES snippet that I could easily copy/paste and attach to the SMILES of the chemical structure it is attached to? Here\ngoes.</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>O1[C@H](C(O)=O)[C@H]([C@H](O)[C@@H](O)[C@@H]1O9)O.\n</code></pre></div></div>\n\n<p>I just realized that <a href=\"https://twitter.com/egonwillighagen/status/1181573810543321088\">the original 3 I used</a> can better be\na <code class=\"language-plaintext highlighter-rouge\">9</code>, which is less likely to occur in the SMILES of the rest of the molecule. The period at the end is also deliberate.\nThat way, I can just copy past the SMILES of the rest directly after that period. Then I get a disconnected structure, but\nI only have to put a 9 next to the atom that is binding to the glucuronide. So, let’s see the R group is methane, I get:</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>O1[C@H](C(O)=O)[C@H]([C@H](O)[C@@H](O)[C@@H]1O9)O.C9\n</code></pre></div></div>\n\n<p>Now, next stop: <code class=\"language-plaintext highlighter-rouge\">CoA</code> and other common biological tags.</p>",
      "summary": "Glucuronide functional group.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/Screenshot_20191008_144049.png",
      "date_published": "2019-10-09T00:00:00+00:00",
      "date_modified": "2019-10-09T00:00:00+00:00",
      "tags": ["chemistry","curation","wikidata","wikipathways","smiles"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}