Recent searches

No recent searches

Search options

Only available when logged in.
mastodon.world is one of the many independent Mastodon servers you can use to participate in the fediverse.
Generic Mastodon server for anyone to use.

Administered by:

Server stats:

8.1K
active users

mastodon.world: AboutStatusProfiles directoryPrivacy policy

Mastodon: AboutGet the appKeyboard shortcutsView source codev4.4.3

#rdkit

0 posts0 participants0 posts today
Greg Landrum<p>Today's <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post shows a way to store partial charges in SD files. We really should stop using mol2 files.</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-07-24-writing-partial-charges-to-sd-files.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/2025-07-24-writing-partial-charges-to-sd-files.html</span></a></p>
Greg Landrum<p>Today's <a href="https://mastodon.social/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RDKit</span></a> blog post is a heartfelt plea for clearer communication.</p><p><a href="https://greglandrum.github.io/rdkit-blog/posts/2025-07-17-naming-similarity-metrics.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/2025-07-17-naming-similarity-metrics.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, 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>
TrendingLive feeds
About