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 tried

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 to

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 and

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, I

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 connets

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 to

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: a

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 material

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 database

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 from

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 new

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 outside

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 supports

Use RDKit from Rust #RDKit #rdkitcffi #Rust

Recently Rust is becoming popular language and I have interest Rust. There is a hurdle for me to move programming language from python to others because I would like to use RDKit from my coding environment for chemoinformatics tasks ;) As many chemoinformaticians know that recently rdkit provides new C Foreign Function Interface (CFFI). And

Create desktop chemoinformatics application with JS #chemoinformatics #RDKit #JS

Long time ago, I wrote post about the same topic. The code used old version of rdkitjs and electron. Recently rdkitjs is maintained in official repository so I would like to re-test the approach. My old post is here. To do the following approach, I installed node.js, electron and npm at first. Then init the

Compare shape and electrostatic similarity of molecules #RDKit #espsim #python

There are lots of way to define molecular similarity, for example fingerprint based, descriptor based, graph based, shape based etc. etc… In the 2D world, circular fingerprint based similarity is used in many case. However, 3D based similarity approach is also useful for drug design. As you now, OpenEye provides useful software named ‘ROCS’. ROCS

Calculate Atom-Atom-Path Fingerprint with RDKit #Chemoinformatics #RDKit

Recently there are lots of publications and codes for feature extraction with GCN of molecules. But fingerprint based approach is still useful due to GCN approach isn’t perfect. I often use the circular fingerprint such as ECFP / MorganFP for machine learning, clustering or other chemoinformatics tasks. Fingerprint based approach is still important I think

Substructure filters for hit triaging #Chemoinformatics #RDKit

This is a second post with jupyter notebook based blog post ;) A simple example of molecular filter which is reported from NIBR! My example code is below. https://iwatobipen.github.io/is_life_worth_living-/jupyter/2021/11/19/NIBR_SF.html

Reinforcement learning with docking score #RDKit #reinvent #chemoinforamtics

Previously I posted automated docking system called dockstream. It supports many compound-protein docking software and recent version of reinvent supports dockstream as scoring method. From the dockstream documentation, reinvent v3.0 supports dockstream but it didn’t work due to some issue of reinvent-scoring which manage scoring function of reinvent. I modified source code to use dockdream

Update RDKit and use new contrib #RDKit #Chemoinformatics

As chemoinformatitians know ;) recently new version of rdkit is released. I appreciate the great work for developpers! One of the interesting point for me is that, FreeWilson(FW) analysis was added to Contrib. FW analysis is a traditional approach of chemoinformatics but I think it’s really MedChem friendly approach. You can get lots of information