Understanding protein-ligand interaction is important for rational drug design. We can use X-ray co crystal structures for SBDD and information of ligand binding site is essential reagion. For example QM/MM approach applies QM level calculation to around binding site and applies MM to far from binding site. QM often offer more accurate energy state butContinue reading “Tool for automated protein-ligand binding site extraction #cheminformatics #Journal #memo”
Tag Archives: memo
Rendering molecular image on Dataframe and Plot with marimo #Memo #RDKit #Cheminformatics
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”
Look Back at 2025 #diary
I’m writing this post at 20:30 ~ JST. I would like to look back at 2025 in my blog post ;) This will be the last post of this year. Thanks for reading. I want to wish you and your family a safe, beautiful and happy New Year.
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”
Contribution for cheminformatics with open science #diary #memo
Recently I could have great opportunity to make hands-on training of cheminformatics. It was fun but really hard task for me to make training material. Thanks colleagues for many kind support ;) In this tutorial, I choiced maize based SBDD pipline building as a topic. I hope every participants enjoyed the session. (I appreciate AZContinue reading “Contribution for cheminformatics with open science #diary #memo”
Generative model with protein embedding as a condition #memo #journal #cheminformatics
Recenlty generative models are widly used not only protein structure generation but also small molecules even if there is still room for improvement. Of course I use them too ;) Today I could have time to test code and read paper, I read an article from JCIM. The tile is “AlphaFold Meets De Novo DrugContinue reading “Generative model with protein embedding as a condition #memo #journal #cheminformatics”
Interesting article from JMC #memo #journal
Last week I could have nice discussion with many people. I feel that current situaion of medicinal chemistry is dramatically changed compared to over 10 years ago. For example, lots of modalities should be considered for developping innovative drugs, lots of informations should be used very rapidly to make decision as soon as possible. SoContinue reading “Interesting article from JMC #memo #journal”
Try to use new LLM phi3 #memo #LLM
As name of LLM means that to use these kinds of models, we need enough GPU memory and it’s not so cost effective for personal use ;) To overcome the limitation, there are lots of technologies are developt and still be developping. LLAMA-cpp is one of the them. Today I would like to share newContinue reading “Try to use new LLM phi3 #memo #LLM”
FW analysis make easily with rdkit contrib FW package #rdkit #chemoinformatics #memo
Last week I enjoyed RDKit UGM 2022. It was really great and exciting evenif I participated there from online. I hope I could participate RDKIT UGM 2023 locally ;) As you know RDKit is one of the useful OSS package for chemoinformatician. It has nice community and be developed actively. I respect the community andContinue reading “FW analysis make easily with rdkit contrib FW package #rdkit #chemoinformatics #memo”
Useful package for ploting chemical space rapidly #chemoinformatics #memo
Visualize chemical space is important task for chemoinformatitian. And there are lots of way to represent chemical space. One of the common approach is PCA. And recently tSNE and UMAP are used. I wrote template code for plotting these data in my task but didn’t write code as a package. Today I found useful packageContinue reading “Useful package for ploting chemical space rapidly #chemoinformatics #memo”
Generate molecules from molecular formula #Chemoinformatics #memo #jcheminf
Most of chemoinformatitian will think that C6H6 means benzene and its SMILES strings will be ‘c1ccccc1’. However how do you think that how many possible combinations will be generated from molecular formula C6H6? ….. Yah, it’s interesting but difficult question. Recently I read interesting article published from Jounral of chemoinformaitcs. The title is ‘Surge: aContinue reading “Generate molecules from molecular formula #Chemoinformatics #memo #jcheminf”
Easy way to visualize SMARTS #chemoinformatics #memo
SMARTS which is a language for describing molecular patterns like regular expression for NLP is really useful for chemoinformatician. However it’s difficult to understand due to difficulty of visualization SMARTS query. As far as I know, there are few software which can visualize beautiful SMARTS pattern. BioSolveIT provides unique SMARTS editor but it’s required commercialContinue reading “Easy way to visualize SMARTS #chemoinformatics #memo”
A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC
Recently there are lots of publications and patents about PROTACs (Proteolysis targeting chimeric). As name indicates that the target of PROTACs is the specific protein of degradation (POI) so it’s called chemical knockdown. Compared to inhibitor, sometime PROTACs shows a strong biological activity. It’s an interesting approach. And I found another interesting approach in ACSContinue reading “A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC”
Get environment SMILES around cutting points #chemoinformatics #memo #RDKit
In this week, I’m in summer vacation but can’t go travel due to COVID19 pandemic and heavy rain. It’s really unusual summer vacation. I hope everyone stay safe. BTW, I often use R-Group decomposition and Matched molecular pairs and these method generate many fragment smiles which has [*] at attachment points. And I would likeContinue reading “Get environment SMILES around cutting points #chemoinformatics #memo #RDKit”
Comparison of rdMMPA cut rules #RDKit #Chemoinformatics #memo
RDKit has code for making mmp in Contrib folder. And also rdkit provides rdMMPA class which can make MMP which is based on user defined cutting rules. Today I checked the rule and modified it with GetSubstructMatches. Default cutting rule is described in rdMMPA document and it’s defined as SMARTS pattern. pattern=’[#6+0;!$(=,#[!#6])]!@!=!#[]’ >> It meansContinue reading “Comparison of rdMMPA cut rules #RDKit #Chemoinformatics #memo”
Read SDF with Multi thread #RDKit #memo #chemoinformatics
In the chemoinformatics task, I often use SDFiles and call SDMolSuppier to read them. BTW, from rdkit version 2020.09.1, Multithreaded file reader for SMILES and SDF is implemented but I’ve never used it. So I used it and compared its speed against default SDMolSupplier. Here is an example. At first I got compound data fromContinue reading “Read SDF with Multi thread #RDKit #memo #chemoinformatics”
Control targeted gene transcription with small molecule #journal #memo
As people well know PROTAC(PROteolysis TArgeting Chimeras) is one of the interesting approach for targeted protein degradation. It has warhead, ligand of targeted protein and ligand of E3 ligase. This bi-functional molecule motif ‘A-Linker-B’ is widely used in drug design. And I read a very interesting article found in my twitter TL. The URL isContinue reading “Control targeted gene transcription with small molecule #journal #memo”
Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics
There are lots of Graph convolutional network(GCN) models are applied for QSAR tasks instead of traditional descriptor based model. The interesting point of GCN is that we don’t need feature engineering I think. It means that during the learning process, GCN learns molecular feature from given molecular graph. On the other side, descriptor based modelContinue reading “Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics”
Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics
Almost 7 years ago, I posted a topics about Lilly’s MedChem filter which is disclosed on github. https://iwatobipen.wordpress.com/2013/08/06/lilly%E3%81%AE%E3%83%95%E3%82%A3%E3%83%AB%E3%82%BF/ It’s interesting for me because most of languages of code on Lilly’s repository are not python and C++, R etc. And one of interesting code is LillyMol. The licence of the code is Apache 2.0. I feltContinue reading “Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics”
Difference between santize mol and not sanitize mol #memo #rdkit
I posted about fast compound search with rdkit. And in the post, I used patternfinger print in the post. Today I checked behavior of the fingerprint. Patternfingerprint can calculate molecules which is not sanitized. However the fingerprint is different to the fingerprint which is calculated from sanitized mol. Here is a simple example. The outputContinue reading “Difference between santize mol and not sanitize mol #memo #rdkit”
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