As lots of readers know that RDKit has useful functions for coding with jupyter-lab. PandasTools and IPythonConsole is useful because by using these functions rdkit can render mol objects as SVG on pandas dataframe. Recently I found that marimo is growing famous as next genration of jupyter-notebook. I recommned to read Pat’s blog post ifContinue reading “Rendering molecular image on Dataframe and Plot with marimo #Memo #RDKit #Cheminformatics”
Tag Archives: python
Split PROTAC molecule to 3 compornents with protac_splitter #RDKit #cheminfomratics #memo #python
Proteolysis-targeting chimeras (PROTACs) are one of the interesting modalities in these days because the modality can engage protein of interest (POI) and E3 ubiquitin ligase and then causes degradation of POI. PROTAC molecules are build from 3 components, POI binder, Linker and E3 binder. So chemists and cheminformatitian would like to analyse these molecules byContinue reading “Split PROTAC molecule to 3 compornents with protac_splitter #RDKit #cheminfomratics #memo #python”
New clustering algorithm for cheminformatics #bblean #cheminformatics #RDKit
Clustering is one of the common but really important task of cheminformatics. There are lots of clustering algorithms are know as readers know, but now we should struggle with huge amount of compound dataset such as Enamine Real, WuXi Galaxy, ZINC and so on in the Era of AI driven drug discovery. It’s becomming taughContinue reading “New clustering algorithm for cheminformatics #bblean #cheminformatics #RDKit”
Useful utils for analysing chemical reaction #cheminformatics #rdkit #rxnutils
Recently lots of users know that generative model of molecule is really useful for drug design. But one of the big challenge is how to make designed molecules. So predicting sythetic route AI is hot topics in these area I think. There are useful retro synthesis AIs are reported such as Spaya.AI, Synthia, Reaxysis, ScifinderContinue reading “Useful utils for analysing chemical reaction #cheminformatics #rdkit #rxnutils”
Use joblib with free-threaded python #memo #diary
Python 3.14 was released on 7 October 2025. The new version of python support for free-threaded (No GIL). I asked it about AI and reasonable description shown below. To understand the merit of “No-GIL” Python (officially known as free-threaded Python), we first need to quickly establish what the Global Interpreter Lock (GIL) is and whyContinue reading “Use joblib with free-threaded python #memo #diary”
Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of course ‘SIMILARITY’ is really difficut term in cheminfomratics. There are lots of metrics for measuring compound similarity.Continue reading “Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics”
Install roshambo2 to pixi env #memo #cheminformatics #RDKit
Recently I’m using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and the code is available under MIT lisence.Articlehttps://pubs.acs.org/doi/10.1021/acs.jcim.5c01322Codehttps://github.com/molecularinformatics/roshambo2/tree/main In this article arthors shows performanceContinue reading “Install roshambo2 to pixi env #memo #cheminformatics #RDKit”
Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo
My background was organic chemistry but now I’m working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I’m interested in the simulation field and openmm and openff are one of my favorite packages to learn MD. OpenMM and OpenFF are developed attractivelyContinue reading “Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo”
Build environment from github repository with pixi #cheminformatics #memo #pixi
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it :) I wrote new package for library management called pixi. In the previous post, I introduced pixi for making new environment. There areContinue reading “Build environment from github repository with pixi #cheminformatics #memo #pixi”
Try to use new package manager for python #pixi #memo
October has arrived, and Japan has become quite cool. It’s a great season for running now. By the way, package management is important task for lots of data scientists. Becase they use lots of packages and each packages depend on other packages. Especially CUDA, I often struggle the issues. Anaconda is one of the usefulContinue reading “Try to use new package manager for python #pixi #memo”
RDKit meets GPU #RDKit #nvmolkit #nvidia #cheminformatics
Unfortunately I could not participate RDKit UGM 2025 in this year…. I would like to join the meeting at next year. By the way, recently we can use GPUs for acceralate chem/bio informatics calculations such as Deep Learning application or clustering tasks. Nvidia’s rapids is one of the famous package for GPU based data science.Continue reading “RDKit meets GPU #RDKit #nvmolkit #nvidia #cheminformatics”
Apply molecular filter more easily #RDKit #Datamol #Cheminformatics
Molecular filter is important for removing unwanted molecules from huge amout of comound dataset. And there are lots of filters are available in these days. For example, PAINS, Role of 5, Role of CNS etc… These filters are publically available but it’s difficult to use from one platform. However datamol, medchem package can support lotsContinue reading “Apply molecular filter more easily #RDKit #Datamol #Cheminformatics”
Useful data preparation package for cheminformatics #RDKit #Aurois #cheminformatics
Data preparation is a really important task in the area of data science. In cheminfomratics tasks, we need curate molecules and properties. One of the my favorite package is chembl_structure_pipeline. Because it is easy to install and has well validated pipeline. The package supports structure preparation but doesn’t data preparation. Today I would like toContinue reading “Useful data preparation package for cheminformatics #RDKit #Aurois #cheminformatics”
Integration Chembl REST API and Claude with MCP #cheminformatics #mcp #ai
Last week I have an opportunity to visit UK for my bussines. I could see beautiful rape blossoms from my way to hotel from Heathrow air port! I participated a workshop as a organaizer and we discussed cutting edge of synergy of human expertise and AI in drug discovery, It was a really wonderful experienceContinue reading “Integration Chembl REST API and Claude with MCP #cheminformatics #mcp #ai”
New Diffusion model based docking tool #MolSnapper #cheminformatics #RDKit
Recently I think relationship between ML and CADD become more closer compared to several years ago. DiffDock is one of the very nice work for interation of cheminformatics and SBDD. It uses diffusion model for protein-ligand pose prediction. But DiffDock can’t run constrain docking which define specific location of protein pocket. Also pure docking toolContinue reading “New Diffusion model based docking tool #MolSnapper #cheminformatics #RDKit”
Experiment of query molecule on RDKit #cheminformatics #RDKit #memo
March is the end of fisical year in most of Japanese company. So I’m busy…. But fortunately I have a time for coding in this weekend. I tested substructure search with RDKit. Substructure query is important for lots of cheminformatics tasks. GetSubstructMatch or GetSubstructMatches are often used I think. BTW, how do you make queryContinue reading “Experiment of query molecule on RDKit #cheminformatics #RDKit #memo”
Template Expansion code of RDKit #memo #cheminformatics #RDKit
Recently lots of compound generative AI codes are available. De novo compound generation approach has potential of generating novel molecules but there are room of improvements for considering synthetic accesibility. So combination of template query and set of side chains approach is good option to enumerate novel molecules with keeping user defined scaffold. RDKit hasContinue reading “Template Expansion code of RDKit #memo #cheminformatics #RDKit”
Determine bond order from XYZ format of molecule #RDKit
As readers know that recent version of RDKit supports XYZ format which is used in quantum chemistry field. The format doesn’t have information of bond order. So to re-construct from the information bond order determination step is required. Recently I found useful function for determining the order in rdkit and Greg wrote useful post almostContinue reading “ Determine bond order from XYZ format of molecule #RDKit”
Run GROMACS from python #MD #BioBB #memo
Happy new year! I hope readers have great end-year holiday. And this is the first post of 2025 of my blog site. My background is medicinal and organic chemistry and cheminformatics. And I’m not so familier with MD(Molecular Dynamics). But recenlty I’m interested in not only informatics but also MD. Recently I found an interestingContinue reading “Run GROMACS from python #MD #BioBB #memo”
Convert molecule object with OpenFFTK #cheminformatics #RDKit #OpenEye #Dry_Advent_Calender_2024
This is my second post for 創薬 (dry) Advent Calendar 2024. 創薬(Souyaku) means ‘Drug Discovery’ in Japanese. Now there are lots of cheminformatics tools are freely available because we can use RDKit and Openbabel as useful OSS for these tasks. BTW, if reader has commercial or academic licence of OpenEye TK, it’s useful too. WhenContinue reading “Convert molecule object with OpenFFTK #cheminformatics #RDKit #OpenEye #Dry_Advent_Calender_2024”
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