Generate molecules with REINVENT and make interactive plot #RDKit #Knime #REINVENT

I introduced to use user defined condaenv in Knime. It’s really useful I think. Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo And as you know, REINVENT is the one of famous compound generation tool for drug discovery. Its community provides lots of example codes as jupyternotebook. After building someContinue reading “Generate molecules with REINVENT and make interactive plot #RDKit #Knime #REINVENT”

Useful python package for QSAR related tasks of chemoinformatician #chemoinformatics #oloren-ai #RDKit

When I posted my memo about open science, @OlorenAI introduced python package named Oloren ChemEngine (OCE). I often use chemprop or interanly build system for QSAR tasks. ChemProp is the one of favorite package because it is easy to use and it includes web application flamework for users. I’ve never used OEC so I triedContinue reading “Useful python package for QSAR related tasks of chemoinformatician #chemoinformatics #oloren-ai #RDKit”

Let’s enjoy open science! #memo #diary

My blogsite was started 2013, so I took almost 10 years ;) It’s amazing. I’m enjoying writing the blog and sharing my code snippet. BTW, I’m working in pharmaceutical company as a chemoinformatician. So, is it risk to write chemoinformatics related post in my blog site….? I don’t think so. As many people know thatContinue reading “Let’s enjoy open science! #memo #diary”

Calculate ligand RMSD with rdkit contrib package #RDKit #memo

Today is the last day of my summer vacation…. Due to COVID-19 pandemic, I and my family didn’t go travel during the vacation however, we’ll go to national championship of dodgeball game in next sturday. It will be exciting day! BTW as you know, rdkit has lots of contrib packages. And I would like toContinue reading “Calculate ligand RMSD with rdkit contrib package #RDKit #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”

Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo

I think workflow tool is useful for many chemoinformatician such as Knime, Pipeline Pilot(PP) and Orange. In my knowledge, it’s difficult to use user defined conda env in PP. Of course these workflow tools provides enough components to do many tasks. But I would like to have more flexibility to build chemoinformatics pipelines. Recently IContinue reading “Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo”

Useful package for virtual screening #chemoinformatics #RDKit

Virtual Screening is important task of drug discovery projects. There are lots of approach for example Finger print based, substructure based and shape based screening. All approaches listed above is not only used in SBDD but also LBDD. And there are lots of apprications to do these tasks. I wrote scripts for these task andContinue reading “Useful package for virtual screening #chemoinformatics #RDKit”

Call RDKit from Rust with conda env ver2 #RDKit #RDKit-sys #Rust #Chemoinformatics

To use rdkit from Rust, I introduced rdkit-sys before. And fortunately recent version of rdkit-sys cleat supports rdkit-env. It’s worth to use conda-env to build rdkit-sys because user don’t need to build rdkit from source code. Following code is almost same as my previous post but I would like to share it. At first, IContinue reading “Call RDKit from Rust with conda env ver2 #RDKit #RDKit-sys #Rust #Chemoinformatics”

Generate molecules with Link-invent #RDKit #RINVENT #chemoinformatics

General molecular generator with deep learning approach is difficult to fix substructure. But common SAR expansion by medchem is focus on specific part such as terminal part, core and linker. Linker is defined as a part which connect parts of molecules. Linker is important of drug design and is called scaffold when the linker connetsContinue reading “Generate molecules with Link-invent #RDKit #RINVENT #chemoinformatics”

Call RDKit from Rust with conda env #RDKit #Rust #Chemoinformatics

I introduced rdkit-sys which is wrapper of rdkit for rust. The package development is ongoing so code is chaged frequentry. To use the package, user need to build rdkit with static link ON option. Build rdkit-sys with static link (.a) is efficient way for portability of the code however it means that it’s difficult toContinue reading “Call RDKit from Rust with conda env #RDKit #Rust #Chemoinformatics”

Run python script in html_file #memo #cording

I wrote lots of chemoinformatics apps as web app. To do that I often use Flask / Django. It’s python packge so most of part can be written in python however it’s difficult to embed python directry in html document. Recently I found cool package for embedding python code in html, it’s name is pyscript.Continue reading “Run python script in html_file #memo #cording”

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”

Use RDKit from Rust v2 #RDKit #Rust

I enjoyed 18th mishima.syk meeting at last weekend. I think the community is really cool and worth to join for caching the cutting edge of chemo/bio informatics ;) Feel free to participate and present here if you have interest the meeting. In the meeting, yamasakit_ introduced “Rust basics” with live coding! Fortunately his presantation materialContinue reading “Use RDKit from Rust v2 #RDKit #Rust”

Make curated Kinase inhibitor dataset from ChEMBL30 #memo #chemoinformatcs

Kinase is one of the attractive target for drug discovery. So there are lots of data not only protein but also inhibitor available. ChEMBL is useful public data source for Kinase inhibitor data however to use the data, we need to retrieve data from the DB and curate it. Of course there are commercial databaseContinue reading “Make curated Kinase inhibitor dataset from ChEMBL30 #memo #chemoinformatcs”

Build peptide from monomer library from ChEMBL #RDKit #ChEMBL #Chemoinformatics

Recently, ChEMBL ver. 30 is released. I’ve installed it in my PC and added rdkit schema ;) And current chembl ftp site provides monomer library of HELM. @magattaca posted really useful blog post in Japanese https://magattaca.hatenablog.com/entry/2020/11/25/004829. The post describes about HELM, its monomer and render these monomers. I’m interested in how to build peptide fromContinue reading “Build peptide from monomer library from ChEMBL #RDKit #ChEMBL #Chemoinformatics”

Make interactive chemical space plot with Dash #RDKit #useful_rdkit_utils #Dash #Chemoinfomratics

Recently I posted really useful package named molplotly. The package can make interactive plot with compound structure as hover. Inspired the activity, I tried to wrote code for making chemical space mapping with interactive rendering of molecules. Base code came from my previous post. There small changes in dash part because of I used newContinue reading “Make interactive chemical space plot with Dash #RDKit #useful_rdkit_utils #Dash #Chemoinfomratics”

Integration of molplotly and Flask for developing chemoinformatics web app #RDKit #molplotly #Flask

Some days ago, @WillMcCorki1 introduced really cool package named molplotly. Thanks for sharing the information. Molplotly is add-on to ploty for rendering molecular image on mouseover like TIBCO Spotfire. The package(https://github.com/wjm41/molplotly) uses JupyterDash for integrating JupyterNotebook so it’s easy to embed interactive chemoinformatics chart in JupyterNotebook. However, it’s difficult to use the package from outsideContinue reading “Integration of molplotly and Flask for developing chemoinformatics web app #RDKit #molplotly #Flask”

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”

Let’s update MMPDB #RDKit #mmpdb #Chemoinformatcs

Matched molecular pairs are popular approach to transform molecules with prior knowledge of medicinal chemistry. MMPDB is useful open source package for managing MMP dataset which is derived from GSK  under the 3-clause BSD license.  It is easy to use and work really fast. I love it the package. However current version of MMPDB supportsContinue reading “Let’s update MMPDB #RDKit #mmpdb #Chemoinformatcs”

Define a function after the request #Flask #memo #python

I love flask and django for making web app and often use Flask for web app development. Sometime the app will serve files after getting user request. In this case, static files which are generated by the app will be stored in static folder. And the folder will store lots of files. So I wouldContinue reading “Define a function after the request #Flask #memo #python”