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#rdkit

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Greg Landrum<p>The new <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post, inspired by a question from Kjell Jorner, looks at the impact of molecular size on similarity thresholds.<br><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-06-20-size-and-similarity-1.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-06-20-size-and-similarity-1.html</span></a></p>
Greg Landrum<p>This week's <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post shows how to use some of the information added to molecules that come from the chemical reactions code.</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-06-12-using-reaction-info.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-06-12-using-reaction-info.html</span></a></p>
Greg Landrum<p>The new <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post is a guest post from <span class="h-card" translate="no"><a href="https://fosstodon.org/@jemonat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>jemonat</span></a></span> with a tutorial on using Bemis-Murcko scaffolds.</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-06-06-murcko-scaffolds.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-06-06-murcko-scaffolds.html</span></a></p>
Greg Landrum<p>This week I have updated and revised an old blog post showing how to perform extended Hueckel calculations with the <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a>. This is a fun one for me because it involves work I did back in grad school. :-)<br><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-05-30-eHT-in-RDKit.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-05-30-eHT-in-RDKit.html</span></a></p>
Greg Landrum<p>This <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post builds on the earlier one about chemical words; this time I'm using Morgan fingerprint bits as the "words".</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-05-22-common-chemical-words-2.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-05-22-common-chemical-words-2.html</span></a></p>
Greg Landrum<p>The new <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog posts demonstrates how to work with your own fingerprints in the PostgreSQL cartridge.</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-05-17-custom-fingerprints-in-postgresql.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-05-17-custom-fingerprints-in-postgresql.html</span></a></p>
Greg Landrum<p>This week's <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post revisits and updates a really old post looking at the most common chemical "words".</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-05-09-common-chemical-words-1.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2025-05-09-common-chemical-words-1.html</span></a></p>
Greg Landrum<p>Hi. I'm a scientist and programmer based in Basel, Switzerland. I'm a long-time advocate of <a href="https://mastodon.social/tags/OpenSource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenSource</span></a> and <a href="https://mastodon.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> and am the primary developer of the <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a>.</p><p><a href="https://mastodon.social/tags/introduction" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>introduction</span></a></p>
Jeremy Monat<p>The 2025_03_1 release of <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> release includes my contribution to speed up part of getting 2D fingerprints for a molecule by ~75x! So if you generate <a href="https://fosstodon.org/tags/chemical" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemical</span></a> fingerprints, now is a good time to upgrade.</p><p>Reminder that I'm <a href="https://fosstodon.org/tags/OpenToWork" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenToWork</span></a> so if you're hiring for <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> or <a href="https://fosstodon.org/tags/scientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>scientificSoftware</span></a> development, let's talk.</p><p><a href="https://fosstodon.org/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://fosstodon.org/tags/DrugDiscovery" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DrugDiscovery</span></a> <a href="https://fosstodon.org/tags/pharma" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pharma</span></a> <a href="https://fosstodon.org/tags/PythonForChemists" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PythonForChemists</span></a></p><p><a href="https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/rdkit/rdkit/release</span><span class="invisible">s/tag/Release_2025_03_1</span></a></p>
Jeremy Monat<p>I'm excited to present "Finding Tautomers" at the first North American <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> User Group Meeting in the <a href="https://fosstodon.org/tags/Boston" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Boston</span></a> <a href="https://fosstodon.org/tags/MA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MA</span></a> area on Friday April 11! </p><p>Reminder that I'm <a href="https://fosstodon.org/tags/OpenToWork" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenToWork</span></a> so if you're in the area and hiring for <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> or <a href="https://fosstodon.org/tags/scientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>scientificSoftware</span></a> development, let me know and we can meet to discuss your needs.</p>
Jennifer Lin<p>Here's a new post on my first encounter with building a simple deep learning model on manually-compiled adverse drug reactions data (thanks to <span class="h-card" translate="no"><a href="https://mstdn.science/@baoilleach" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>baoilleach</span></a></span> for feedback) - <a href="https://jhylin.github.io/Data_in_life_blog/posts/22_Simple_dnn_adrs/2_ADR_regressor.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jhylin.github.io/Data_in_life_</span><span class="invisible">blog/posts/22_Simple_dnn_adrs/2_ADR_regressor.html</span></a></p><p>Notes re. data - <a href="https://jhylin.github.io/Data_in_life_blog/posts/22_Simple_dnn_adrs/1_ADR_data.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jhylin.github.io/Data_in_life_</span><span class="invisible">blog/posts/22_Simple_dnn_adrs/1_ADR_data.html</span></a></p><p><a href="https://fosstodon.org/tags/PyTorch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PyTorch</span></a> <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> <a href="https://fosstodon.org/tags/ChEMBL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ChEMBL</span></a> <a href="https://fosstodon.org/tags/embeddings" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>embeddings</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Greg Landrum<p>There's a new <a href="https://sciencemastodon.com/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post introducing some new functionality that I'm really excited about: doing efficient substructure and similarity searches in very large chemical libraries:<br><a href="https://greglandrum.github.io/rdkit-blog/posts/2024-12-03-introducing-synthon-search.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2024-12-03-introducing-synthon-search.html</span></a></p>
Greg Landrum<p>Yes! <a href="https://sciencemastodon.com/tags/rdkit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>rdkit</span></a></p>
Jeremy Monat<p>As the YouTubers would say, “A lot of you have been asking me about how to write <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> blog posts.” Well, not a lot, but at least a couple! Here's my process. <a href="https://bertiewooster.github.io/2024/11/21/Cheminformatics-Blogging-How-To.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bertiewooster.github.io/2024/1</span><span class="invisible">1/21/Cheminformatics-Blogging-How-To.html</span></a> <br><a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a> <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> <a href="https://fosstodon.org/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a></p>
Chris Swain<p>A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design <a href="https://macinchem.org/2024/11/23/shepherd-shape-electrostatics-and-pharmacophore-explicit-representation-diffusion/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">macinchem.org/2024/11/23/sheph</span><span class="invisible">erd-shape-electrostatics-and-pharmacophore-explicit-representation-diffusion/</span></a> <a href="https://sciencemastodon.com/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://sciencemastodon.com/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a></p>
Andrew Dalke<p>Just announced "talus - tools to make SMARTS-based <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> fingerprints" to the <a href="https://toots.nu/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> mailing list.</p><p><a href="https://hg.sr.ht/~dalke/talus" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">hg.sr.ht/~dalke/talus</span><span class="invisible"></span></a></p><p>I'm able to process SMILES file -&gt; Klekota-Roth SMARTS-based fingerprints at about 12.5x baseline speed.</p><p>RDMol -&gt; fingerprints performance is 13.2x baseline.</p><p>It includes some SMARTS analysis methods to tell if a SMARTS atom pattern X is a subset of a SMARTS atom pattern Y.</p>
Chris Mungall<p><span class="h-card" translate="no"><a href="https://sciencemastodon.com/@dr_greg_landrum" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>dr_greg_landrum</span></a></span> I'm sure I'm doing something either quite naive or unoriginal here (I'm a <a href="https://genomic.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> newbie). <span class="h-card" translate="no"><a href="https://scholar.social/@cthoyt" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>cthoyt</span></a></span> says you have likely looked into this.</p>
Chris Mungall<p>Exploring using LLM generating <a href="https://genomic.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> programs to auto-classify chemical structures. Initial results seem quite good (but not as good as ClassFire), but plenty room for improvement. <a href="https://github.com/cmungall/chebi-llm-classifier/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/cmungall/chebi-llm-</span><span class="invisible">classifier/</span></a></p>
Jeremy Monat<p>Why do some organic molecules have a color? It's usually because of a long chain of conjugated bonds. In my <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> blog post, I search 20K datapoints to find a series of molecules where extending the conjugated chain increases the absorption wavelength. <a href="https://bertiewooster.github.io/2024/10/15/Color-from-Conjugation.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bertiewooster.github.io/2024/1</span><span class="invisible">0/15/Color-from-Conjugation.html</span></a> <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a> <a href="https://fosstodon.org/tags/Polars" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Polars</span></a> <a href="https://fosstodon.org/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://fosstodon.org/tags/greatTables" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>greatTables</span></a> <a href="https://fosstodon.org/tags/Altair" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Altair</span></a></p>
Greg Landrum<p>Here's the next <a href="https://sciencemastodon.com/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post about new stuff in the recent 2024.09.1 release:<br><a href="https://greglandrum.github.io/rdkit-blog/posts/2024-10-10-whats-new-2024-09-2.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">greglandrum.github.io/rdkit-bl</span><span class="invisible">og/posts/2024-10-10-whats-new-2024-09-2.html</span></a></p>
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