10 Mar 2026, 14:58 UTC873 views16 reactionsread 23 August 2026 If you're teaching chemoinformatics or drug design, this could be of interest to you. UCL published tutorial and Jupyther notebooks on docking using SMINA. Bare minimal, but it looks like important information is present, including presentation.
https://github.com/UCL/Open_Docking_Lab_Handbook
⚡9👍6❤1
Signed Timur Madzhidov
5 Mar 2026, 22:14 UTC≈1,020 views3 reactionsread 23 August 2026 Raymond lab decided to go further after GDB-17 and decided to collect GDB-20! The size is obviously too large 32 trillion structures, so they sampled subset by “GenerativeAI”. As to me, even their GDB-17 was a big crazy idea however it helped to understand how weird are randomly generated structures. But GDB-20… looks to me as an artefact of the epoch went for good… but great that this time they provide access to 12 …
👍3
Signed Timur Madzhidov
23 Jan 2026, 09:01 UTC≈1,280 views5 reactionsread 23 August 2026 Wendi Warr shared her free report from the 2025 CINF Herman Skolnik Award symposia celebrating contribution of Professor Matthias Rarey. Quite interesting reading mostly about structure-based drug design.
#SBDD
https://drive.google.com/file/d/1aZcHqy07mSQKaq7My-R8WVjrXD1I6YPg/view
👍5
Signed Timur Madzhidov
17 Nov 2025, 13:59 UTC≈1,490 views12 reactionsread 23 August 2026 Quite a nice and helpful open source tool - the Python code for finding pockets in proteins. Intsallable via pip and GitHub. #SBDD #bioinformatics #openscience #docking
GitHub
https://github.com/cch1999/pocketeer
Article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-168
🔥7❤5
Signed Timur Madzhidov
21 Oct 2025, 07:51 UTC≈1,330 views11 reactionsread 23 August 2026 Photo
I think this tool could be rather useful for those who work in the drug design and especially structure based drug design. PocketMaster is a flexible and automated tool for analyzing, clustering, and visualizing protein binding sites.
Main Functionalities of PocketMaster
✅ Automatic structure alignment
✅ Flexible methods for defining binding sites
✅ Support for multiple RMSD methods
✅ RMSD calculatio…
❤9👍2
Signed Timur Madzhidov
20 Oct 2025, 08:09 UTC846 views4 reactionsread 23 August 2026 Grzybowski work shows how they used rather cheap robot for doing quite fancy study of reactivity and catalyst design. Rather interesting reading as to me but more from the point of view what could be done, and how insights can be gathered. Some code was open-sourced too, which look rather new for Grzybowski lab, good direction to go! #robochemistry #chemicalspace
https://www.nature.com/articles/s41586-025-09490-1
👍2❤1🔥1
Signed Timur Madzhidov
20 Oct 2025, 08:04 UTC690 views11 reactionsread 23 August 2026 MIT work on prediction of solubility in mixture of solvents. No rocket science or fancy ML as to me, just a well done work. But the model and data available.
https://www.nature.com/articles/s41467-025-62717-7
❤🔥5❤2💊2👍1🔥1
Signed Timur Madzhidov
3 Aug 2025, 18:36 UTC995 views3 reactionsread 23 August 2026 And adding to previous post. Kevin has just published (in September 2025, does he have time machine?) a paper on problems of testing LLMs. For the first time in my carrier I read it more like a scream from author's soul. Ok, there were articles like this on data reproducibility, but this one I take more personally, probably.
#LLM
https://www.sciencedirect.com/science/article/pii/S0927025625003842
BTW, it worth also…
❤2👍1
Signed Timur Madzhidov
3 Aug 2025, 18:23 UTC761 viewsread 23 August 2026 Startup Harmonic develops AI chatbot for math reasoning with the idea to develop "mathematical superintelligence" (https://www.techticia.com/2025/07/harmonic-launches-aristotle-ai-chatbot.html). It is interesting when will we come to LLM that is on par with human in chemistry reasoning? So, far works of Philippe Schwaller and Kevin Jablonka show that LLM struggle in reasoning in chemistry domain. But it is amazing, t…
Signed Timur Madzhidov
23 Jul 2025, 12:48 UTC897 viewsread 23 August 2026 Interesting benchmark of different neural network potentials (NNPs) to predict protein-ligand interaction energy. They used NNPs trained on materials-science data (Orb-v3 and MACE-MP-0b2-L), specific models for predicting certain biological targets (Orb-v3) and six NNPs trained on molecular data (ANI-2x, AIMNet2, Egret-1, eSEN-OMol25-sm-conserving, UMA-s, and UMA-m). For comparison, semi-empirical DFT (GFN2-xTB and g…
Signed Timur Madzhidov
22 Jul 2025, 13:35 UTC≈1,340 views14 reactionsread 23 August 2026 Photo
Really cool tool was released by Rarey group: the list of 40 000 (!) functional group SMARTS and corresponding software that gives a list of groups that present in a molecule. The application is run as backend service, which I don't really like but can be helpful in some applications. But what is great - that SMARTS and their labels are available in csv file of the GitHub. That's supercool thing.
Paper: https://pubs…
👍7❤4🔥3
Signed Timur Madzhidov
16 Jul 2025, 06:36 UTC857 views14 reactionsread 23 August 2026 Amazing publication from Frank Noe and Microsoft Research team: generative model that predicts ensemble of peptide conformations. Basically, it is generative model that returns MD results at the costs of an hour. What a time we live in!
Abstract:
Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu,…
❤7👍4🔥3
Signed Timur Madzhidov
Showing the 12 most recent of 18 posts we hold for @chemoinfo_papes. View and reaction counts are the latest single reading for each post, not a live figure, and a recent post is still accumulating both. A view count marked ≈ was rounded by Telegram before we ever saw it — t.me prints views in full below 1,000 and to three significant figures above, so ≈1,200,000 means somewhere between 1,150,000 and 1,249,999. Unmarked counts are exact. Text is reproduced from the public post preview and truncated for length.