Look Back at 2021 #diary

I’m writing the post on the Shinkansen. Counting from 2020, we’re still in the COVID-19 pandemic. My life style is dramatically changed before / after the pandemic. But still continuing the blog ;) Here is the access log of the site. There are more unique visitors (deep blue bars) in 2021 compared to the last

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 torsion drive results between C and O linker of specific structure #qcportal #souyakuAC2021

I wrote a Japanese post about PAM/NAM about mGlu family yesterday. As I mentioned that, small difference of molecules makes big difference of these conformations. I tried to check it with ETKDGv2 method which is implemented in RDKit. The approach is based on Molecular Mechanics(MM) so I would like to check it not only but

ACSのOpen accessのジャーナルから2021冬 #souyakuAC2021 #Japanese-post

最近何故か複数のサイトを管理しているiwatobipenです。ちなみにこのサイトのBlog更新頻度が低下しているのはそのせいではなく、純粋に忙しいためです。今年も残り後少し、早いものですね。 そして今年もまたAdventCarenderの季節になりました。 私はOSSやOpen Accessのジャーナルが好きです。もちろん職場でも自宅でも利用できるということもありますがそれ以上に良いコミュニティーが形成されているものが残るからです。さて、今日はACS系のジャーナルでOpen Accessのもので最近気になったものを紹介させてもらおうと思います。ACS Bio & Med Chem Au というジャーナルでACS系においては珍しくアクセスフリーです。カバー範囲もライフサイエンス系です https://pubs.acs.org/doi/10.1021/acsbiomedchemau.1c00033This includes experimental and theoretical studies on the chemical, physical, mechanistic, and/or structural basis of biological or cell function across all domains of life. で今回読んだのは以下の論文です。 Title ’Discovery of “Molecular Switches” within a Series of mGlu5 Allosteric Ligands Driven by a “Magic Methyl” Effect Affording Both PAMs and

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

A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC

Recently there are lots of publications and patents about PROTACs (Proteolysis targeting chimeric). As name indicates that the target of PROTACs is the specific protein of degradation (POI) so it’s called chemical knockdown. Compared to inhibitor, sometime PROTACs shows a strong biological activity. It’s an interesting approach. And I found another interesting approach in ACS