Use SAPT/FISAPT more easily #chemoinformatics #psikit #quantumchemistry

Now I’m developing new method for psikit. So this new function is not imlemented in original repository yet but I checked it in my repo. The new method is named SAPT. Symmetry-adapted perturbation theory (SAPT) provides a means of directly computing the noncovalent interaction between two molecules. And as same as fragment orbital method(FMO)’s PIEDA

Move your Building Block shelf from internal to external! #memo #journal #medchem

When I try to build compound library with parallel chemistry, collecting the Building Blocks and weighting is very time consuming part. And also it will take long time if the required building blocks are not available in internal reagent shelf. There are some services are provided from reagent vendors which they weights reagents and delivers

Detect outlier with Isolationforest #chemoinformatics #scikit-learn #RDKit

Applicability domain(AD) is often discussed in chemoinformatics for QSAR. Because current QSAR often can’t predict unsimilar compounds against training set. The definition of unsimilar is often used with tanimoto similarity with molecular fingerprint. So QSAR model user need to take care about where new designed molecule in the model AD or not. Some days ago,

New fluolination reaction from JACS #memo #organicchemistry

Trifuloromethylation is useful reaction in drug discovery. Because CF3 and other fluorinated substituent are often used in drug like molecules. It is also useful that the reaction can conduct in asymmetric manner. I read interesting article in JACS today published by Trost’s group. The URL of the article is below.https://pubs.acs.org/doi/10.1021/jacs.9b06231 You can see abstract without

Run rdkit on cloud #RDKit

This is the first post of my new PC with linux env. Recently I decided to move from MacBookPro(MBP) to Dell XPS15. Because recent MBP doesn’t have nvidia GPU…. It is not so attractive for me. So I got XPS15 which has win10 as default OS. I removed Win10 ASAP and installed ubuntu 18.04. Now

Let’s teleportation! #Quantumcomputing #qiskit #memo

Recently I am learning quantum computing and qiskit coding.Learning new things is very fun for me. Today I tried to code quantum teleportation with qiskit. ’Teleportation’ sounds attractive for me I watched many SF movies when I was child ;) BTW, definition of teleportation is ‘the ability to transport a person or object instantly from

Node feature importance of Graph convolutional neural network #chemoinformatics #memo

I wrote blog post about GCN with pytorch_geometric before.https://iwatobipen.wordpress.com/2019/04/05/make-graph-convolution-model-with-geometric-deep-learning-extension-library-for-pytorch-rdkit-chemoinformatics-pytorch/ Recently graph based approach is very hot area in chemoinformatics I think. Lots of articles are published with new architecture. However there are few discussions about node features. Recently I am thinking about the importance of node feature. Today I checked it with very simple code.

Photredox reaction on DNA #memo #chemistry

Today I found very interesting article from researchers who is working at pfizer and Hitgen. https://pubs.acs.org/doi/10.1021/acscombsci.9b00076 Pfizer and Hitgen launched drug discovery collaboration two years ago.https://www.genengnews.com/topics/drug-discovery/pfizer-hitgen-launch-drug-discovery-collaboration/ Hitgen is one of CRO with DNA-encoded library as core technology. In the article the authors reported that they conducted photoredox reaction on DNA tag. Photoredox reaction is very

SVM on quantum computing! #quantumcomputing #qiskit

Support vector machine is one of major method of machine learning. It very useful and powerful algorithm. However, SVM is not suitable for large size dataset. Recently I’m learning QISKIT and qiskit has an attractive method named QSVM. It means that perform SVM on quantum circuit! Dose it sound fun? Original URL of the paper

Make quantum accumulator #quantum computing #qiskit

It’s not related to today’s topic but I’m sick with back pain. I hope I will get well soon.. Somedays ago I wrote post about qiskit. I think qiskit is very interesting package for quantum computing. And I stared to learn qiskit and quantum computer. One of the interesting point of quantum computer is that