This is a post for 創薬 (dry) Advent Calendar 2024. 創薬(Souyaku) means ‘Drug Discovery’ in Japanese ;) The advent calendar is organised by Souyakuchan who is famous idol of drug discovery in Japan. She contributes drug discovery with open science and social network. It’s really interesting work! I introduced Metis which is UI for HumanContinue reading “Simple Voting system for molecule #cheminformatics #RDKit #Dry_Advent_Calender_2024”
Tag Archives: python
Useful package for collecting MedChem’s feedback #RDKit #Cheminformatics #Metis
Recently there are lots of activities about accelerate Drug Discovery with AI reporeted from not only BioTech but also pharmaceutical company. To use Genenerative AI in Small molecule project, scoring function definition is really difficult but important task. Because Gen AI can not understand chemists preference (drug likeness in another word) correctly sometime. To overcomeContinue reading “Useful package for collecting MedChem’s feedback #RDKit #Cheminformatics #Metis”
Try to use new method of rdkit202409beta #RDKit #Cheminformatics #memo
I really thanks to oragnizer, all presenters and all participants of RDKit UGM2024 held at Zurich in last week ! As same as previous meeting, it was really cool and interesting meeting. Hybrid style of the meeting is very kind for not only in-person participants but alos on line participants I think. It’s difficult toContinue reading “Try to use new method of rdkit202409beta #RDKit #Cheminformatics #memo”
New and fast clustering algorithm of chemical libraries #cheminformatics #rdkit #clustering
Clustering librariries is one of the common but important task of cheminformatics. For example if you need to pick molecules from large amount of compound set, cluster these molecules and pick top X molecules will be one of the strategy. But in case of large compound set, clustering will be hard task ;) As youContinue reading “New and fast clustering algorithm of chemical libraries #cheminformatics #rdkit #clustering”
Use DiffDock as web application #DiffDock #cheminformatics #memo
As many readers know that DiffDock is one of the famous Deep Learning based docking program which use diffusion model. It was published 2022 at arxiv and code is disclosed on github. Recenlty I found that the repository was updated and code for web application is added :)https://github.com/gcorso/DiffDock I interested it because web app isContinue reading “Use DiffDock as web application #DiffDock #cheminformatics #memo”
New cheminformatics package for Molecular Alignment and 3D Similarity Scoring #cheminformatics #rdkit #memo
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 are more limited. Recently I found attractive articles at ChemRxiv.ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring Roshambo has not only CLI but alsoContinue reading “New cheminformatics package for Molecular Alignment and 3D Similarity Scoring #cheminformatics #rdkit #memo”
Open source structure preparation package for small molecule virtual screening #RDKit #OSS #Cheminformatics
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 protonate state, enumerate chirality, tautomer and stereo isomer if necessary. There are lots of OSS libraries which can generate 3D conformers from SMILES such asContinue reading “Open source structure preparation package for small molecule virtual screening #RDKit #OSS #Cheminformatics”
New approach for selecting building blocks from reagent set #RDKit #memo #cheminformatics
At hit to lead(H2L) stage in drug discovery projects, some attractive scaffolds are indentfied and explore SAR activity. And efficient method to select R-Groups from reagent list is requred as cheminformatics / CADD tasks. Selection requirements are variable, for example to get diversity, to keep exit vector and to get novelity etc. It depends onContinue reading “New approach for selecting building blocks from reagent set #RDKit #memo #cheminformatics”
Predict pKa value with ML&QM #memo #cheminformatics #RDKit
pKa value is one of the important parameter in drug design. It’s describes basicity and acidity of molecules. So there are lots of tools to predict pKa value such as ACD lab, Marvin etc. Compared to commercial packages there are few solutions in open science field. Paul Crodrowski’s group disclosed code for pKa prediction onContinue reading “Predict pKa value with ML&QM #memo #cheminformatics #RDKit”
Try to make SBDD work flow with Flow Based Programming(FBP) #cheminformatics #SBDD #RDKit #python
If target structure of the drug discovery project is available, SBDD is one of the practical approach. Docking study is common method of SBDD. There are lots of docking simulation softwares recently not only commercial packages but also open source software. AutoDock Vina is one of the famous Docking tool in the area. To runContinue reading “Try to make SBDD work flow with Flow Based Programming(FBP) #cheminformatics #SBDD #RDKit #python”
Add hydrogen with user defined pH from python #openbabel #cheminformatics
As many cheminformaticians know that Openbabel is one of the famous and useful package of Cheminformatics as same as RDKit. Openbabel provides not only CLI but also API for some programming languages including python of course ;). Openbabel can protonate molecule with user defiened pH. The function is not available from current version of RDKit.Continue reading “Add hydrogen with user defined pH from python #openbabel #cheminformatics”
Generate new molecules from fragments with Diffusion model #cheminformatics #rdkit #difflinker #memo
Designing linked molecule from fragments is one of the important task for drug desing such as FBDD, Scaffold hopping (e.g. replace core) and PROTAC molecule design. As readers know there are lots of solutions to do it, for examoke BROOD is one of the famous commercial package for fragment replacement. I can’t use commercial packageContinue reading “Generate new molecules from fragments with Diffusion model #cheminformatics #rdkit #difflinker #memo”
Edit atom indices of RDKit Mol object #memo #cheminformatics
Atom indecies are unique number of each atom. And RDKit adds the index when mol object is generated. RDKit makes mol object from SMILES, Inchi, molblock and lots of formats. To make canonical representation of molecules, the atom indices are asigned allways same roules in automatically. The indices are asigned regardless of scaffold. So ifContinue reading “Edit atom indices of RDKit Mol object #memo #cheminformatics”
Current status of DMTA cycle in AZ #memo #DDT #publication #AI/ML
March is end of fiscal year in most of Japanese company. I spent lots of time for paper work in these days… ;P As many readers know that, DMTA cycle is key of drug discovery/optimization process and lots of computational and high thoughput experimental apporaches are available in the process recenlty. I think AZ isContinue reading “Current status of DMTA cycle in AZ #memo #DDT #publication #AI/ML”
Predict protein-ligand complex dynamics with python #dynamicbind #cheminformatics #memo
Computer aided drug design is one of the powerful approach for drug discovery these days. Docking study of target protein and ligands is common proceduer to evaluate whether the compound fit target protein’s pocket or not. However there is a limitation in the method. Most of the docking apporach handle protein and ligand as rigidContinue reading “Predict protein-ligand complex dynamics with python #dynamicbind #cheminformatics #memo”
Update rdkit/shape-it #RDKit #shape-it #cheminformatics
Today I tried to build rdkit/shape-it because I could not build shape-it with current version of rdkit. So I struggled error message to fix the issue.(I’m not so good at C++ ;P) There are two issues in the current code.1. Version of c++ in the CMakeLists.txt is old, so I changed it from c++14 toContinue reading “Update rdkit/shape-it #RDKit #shape-it #cheminformatics”
Visualize feature importance with marimo #cheminformatics #RDKit #marimo
I posted new generation of notebook, marimo recently. It is cool and easy to make interactive analysis environment with python. I’m interested in the package and am thinking how to use in chemoinformatics tasks. In QSAR tasks, chemoinformaticians are often asked the reason of prediction of the model. So XAI (explainable AI) is an attractiveContinue reading “Visualize feature importance with marimo #cheminformatics #RDKit #marimo”
New ML package for cheminformatics #cheminformatics #QSAR #ML
I introduced scikit-mol in my blog post before. The package integrates scikit-learn and rdkit. It’s easy to use because user can build QSAR model from scikit-learn’s API. I like the package. And recently I found another useful package for cheminformatics named ‘molflux‘ witch is developed by researchers in Exsicentia, famous AI Drug Discovery pharma. molfluxContinue reading “New ML package for cheminformatics #cheminformatics #QSAR #ML”
New type of python notebook #marimo #cheminformatics #RDKit
Jupyter-lab, Jupyter-note book, streamlt and other packages are useful for data science beucase it can analyze and visualize data step by step. I like streamlit and dash for making simple web app. And some days ago I found new and cool package named marimo. From the documentaion, marimo is an open-source reactive notebook for Python — reproducible,Continue reading “New type of python notebook #marimo #cheminformatics #RDKit”
Try to use mmpdb v3.1 #RDKit #MMPDB #cheminformatics
As many RDKitters know that Andrew released new version of MMPDB! Recent version of MMPDB has lots of useful methods, one of the generate method it can generate new molecules from given smiles. The method can generate not only all possible molecules from MMPDB but also constrained molecules with options, ‘–query’ and ‘–constant’. ‘–query’ optionContinue reading “Try to use mmpdb v3.1 #RDKit #MMPDB #cheminformatics”
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