Quantum computing for chemistry #RDKit #psi4 #qiskit

Some years ago I read book about quantum computing written in Japanese. https://www.amazon.co.jp/%E9%87%8F%E5%AD%90%E3%82%B3%E3%83%B3%E3%83%94%E3%83%A5%E3%83%BC%E3%82%BF%E3%81%8C%E4%BA%BA%E5%B7%A5%E7%9F%A5%E8%83%BD%E3%82%92%E5%8A%A0%E9%80%9F%E3%81%99%E3%82%8B-%E8%A5%BF%E6%A3%AE-%E7%A7%80%E7%A8%94/dp/4822251896 It was very exciting for me and I had interested in quantum computer. Quantum computer has potential to solve many difficult problems for conventional computer. Of course it is useful for chemistry. You know qiskit is one of python library for quantumContinue reading “Quantum computing for chemistry #RDKit #psi4 #qiskit”

An article about fluorine #memo #medchem #journal

Recently there are many drugs that contain fluorine atom. Fluorine atom is often used in medicinal chemistry to improve potency, metabolic stability reduce toxicity etc. And the recent progress of chemistry enable to introduce fluorine atoms in many position of molecule. You know, there are many fluorination reagents. Fluorine atom is familiar to medicinal chemists,Continue reading “An article about fluorine #memo #medchem #journal”

GetTanimtoSim/DistMat as a lower triangular matrix and convert 2D array #RDKit #Chemoinformatics

Similarity / Dissimilarity matrix is often used for not only checking the bulk of molecular similarity but also the chemical space (such as MDS). The cost of pair similarity matrix is O(N^2). After calculation, I can get N x N similarity / dis similarity matrix. I found some functions to calculate similarity metrics in rdkitContinue reading “GetTanimtoSim/DistMat as a lower triangular matrix and convert 2D array #RDKit #Chemoinformatics”

QSAR toolbox for myself #RDKit #Chemoinformatics

I often work with SDF to build some QSAR models. Data preparation process is almost same. So I decided to make tool box for myself. It is not complex code, very simple.https://github.com/iwatobipen/QSAR_TOOLBOX Current code has two main scripts. One is finger print generator and another is model builder and optimizer which make SVM, RF andContinue reading “QSAR toolbox for myself #RDKit #Chemoinformatics”

The last piece of gem-difluorocycloalkans #medchem #memo #journal

Recently fluorination is one of an important strategy in medicinal chemistry, it sometime improves not only potency but also any ADMET profiles. Yes I like fluorination strategy ;) However fluorination reaction is needed very harsh conditions. So I think fluorinated building blocks are very useful for medicinal chemistry to avoid such as harsh reaction stepsContinue reading “The last piece of gem-difluorocycloalkans #medchem #memo #journal”

Psikit update/Draw ESP, HOMO LUMO #RDKit #Chemoinformatics #quantumchemistry

I just updated psikit which is package for quantum-chemoinformatics ;) It can be installed from conda / pypi :) I added and updated new function for molecular property rendering. Current version of psikit can draw not only frontier orbital but also ESP and dual descriptor. Dual descriptor is calculated by psi4. What is dual descriptor?Continue reading “Psikit update/Draw ESP, HOMO LUMO #RDKit #Chemoinformatics #quantumchemistry”

Nice review about ML for drug discovery #memo #chemoinfomatics

Here is a nice review of Machine learning(ML) in drug discovery. If reader has interested in ML and drug discovery, I recommend to read the article ;) https://www.nature.com/articles/s41573-019-0024-5 The article describes how ML is used in drug discovery. Recently DL is used in wide are in drug discovery target identification and validation, compound screening andContinue reading “Nice review about ML for drug discovery #memo #chemoinfomatics”

Enumerate partial heteroaromatic rings in a molecule #RDKit #Chemoinformatics

I posted hetero shuffling before. It worked well but redundant. There is a nice code in RDKit UGM2017 material. URL is below. https://github.com/rdkit/UGM_2017/blob/master/Notebooks/Cole-Enumerate-Heterocycles.ipynb The code defined transformation with hard coding and seems nice. In case of real project, we sometime would like to do enumeration against partial substructure not all structure. I thought how toContinue reading “Enumerate partial heteroaromatic rings in a molecule #RDKit #Chemoinformatics”

Constrain Embedding with MCS as a core #RDKit #Chemoinformatics

Recently I’m struggling to generate 3D structure with RDKit. I would like to generate constrained 3D structure of target molecule with reference molecule. You know, there are very nice articles are found in RDKit blog site. URLs are below.http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.htmlhttp://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html These posts are describing how to use ConstrainedEmbed and EmbedMolecule with coorMaps option. ConstrainedEmbed method. RegardingContinue reading “Constrain Embedding with MCS as a core #RDKit #Chemoinformatics”

Hetero shuffle and halogen replacement of molecule #RDKit #Chemoinformatics

I posted comparison of rdChemReactions and EditableMol before. In the post I wrote rdChemReaction could not keep position of original molecule. But…. It is due to my wrong query. Today I checked some function of RDKit. I tried to replace aromatic carbon to nitrogen and replace hydrogen which is attached aromatic carbon to fluorine andContinue reading “Hetero shuffle and halogen replacement of molecule #RDKit #Chemoinformatics”