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"| Is life worth living?
Most of readers know that power of GPU changes the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in sho…| Is life worth living?
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 cal…| Is life worth living?
I am enjoying a weekend with free time for the first time in a while :)And I checked my blog site and found that I stared the site from 2012/08/10. So it means that I’ve kept writing blog for almost 13 years. When I stareted the blog post I was a wet medicinal chemist butContinue reading "Contribute open science #memo #dirary"| Is life worth living?
I spent really busy summer vacation in this year. So it was difficult to make time to post the blog ;-) Today I could have time to write short post. So I wrote new post, thank you for reading as al…| Is life worth living?
Japanese summer is very hot and humid most days. It’s not so good for running.It’s important to stay hydrated. I’m keeping my lunch time 5km Running when I work from home. I could…| Is life worth living?
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 C…| Is life worth living?
Recently I have interest to MCP. Because MCP can engage task and API with natural language so we don’t need code (BTW, I love writing code!!!!). Today I tried to make SQL query with MCP. I us…| Is life worth living?
GAMESS is one of the major program of open source program of quantum chemistry. My former boss is QC/QM expart and I learned usefullnes of GAMESS. So I like GAMESS but recently I don’t have o…| Is life worth living?
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"| Is life worth living?
Shape based alignment approach is useful for LBDD which is not available for target protein structure. However there are few OSS to align molecules like OpenEye’s ROCS. Also GPU based tools a…| Is life worth living?
In the cheminformatics area we often use SMILES wich is 1D representation of molecules. But to conduct virtual screening we should prepare molecules from SMILES to 3D structure whith predict proton…| Is life worth living?
