Development of new force field

Molecular force fields development is required human time and expertise. Comp Chemists often uses FF for their task. So force field is key parameter to conduct calculations. But it has still room for improvement. I have not know that major FF, AMBER-family does not have access to bond order information. Recently I read an articleContinue reading “Development of new force field”

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Calculate HOMO and LUMO with Psi4 reviced #RDKit #Psi4

Yesterday, I got comments from reader. Regarding the comment, to calculate HOMO LUMO with psi4 correct way is below. Next, calculate HOMO-LUMO of benzene with the function and psi4. After the calculation, I could access HOMO-LUMO, the code is below. Check log file That’s all. I am happy because I can get many response throughContinue reading “Calculate HOMO and LUMO with Psi4 reviced #RDKit #Psi4”

Calculate HOMO and LUMO with Psi4 #RDKit #Psi4

You know Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. It is very easy to use and has an optional Python interface. It is useful for us I think. Because Psi4 can use in python, it means we can integrate manyContinue reading “Calculate HOMO and LUMO with Psi4 #RDKit #Psi4”

Dual Kinase inhibitor for Autoimmune disease

There are lots of JAK/TYK inhibitor project in drug discovery area. https://www.ncbi.nlm.nih.gov/pubmed/30113844 Here is an article from pfizer. Pfizer discovered and launched JAK inhibitor ‘tofacitinib’. Tofacitinib inhibits JAK3, JAK1 and JAK3. It is well known that JAK2 uniquely forms a homodimer, which is important in hematopoiesis via signal transduction associated with erythropoietin (EPO), thrombopoietin (TPO),Continue reading “Dual Kinase inhibitor for Autoimmune disease”

第17回 サマーカップinエコパの応援行った #ドッジボール

 長男が所属しているドッチボールチームの参加する大会、第17回 サマーカップinエコパ ということで、掛川のエコパアリーナまで応援に行ってきました。 http://www.shizuoka-dba.com/keikaku.html  今年は低学年の入団者が多く、オフィシャル1チーム、ジュニア2チーム、計3チームでの参戦でした。長男はチームに所属してちょうど一年くらい。今回はジュニア、1,2年生メインのチームでアタッカーとして頑張っていました。 ドッジボールのジュニアは4年生以下の小学生で構成されます。4年生がいるチームと比べると今回のチームはまだまだ小柄な子が多く、予選リーグを突破することはかないませんでしたが、高学年相手に果敢にボールを投げアウトを取ったり、相手のボールをキャッチしている姿を見ると、家でがグズグズしてるが成長してきたなって思いました。 他の子も、みんな元気に頑張ってました。頼もしい!  オフィシャルともう一つのジュニアはいずれも決勝リーグに勝ち残りましたが、残念ながら優勝には届かず。チームの仲間と力を合わせて勝利を目指す姿を見るのはこっちも元気をもらって、とても楽しいものです。  豪速球を投げるエースがいるチームは迫力がありますし強いですがそれだけでは勝ち残れないのがまた面白いところ。5分という短い時間での逆転劇などスリルもあるし面白い。 まだまだ暑い夏が続きますが、体調を崩さず元気に楽しく頑張ってほしいものです。 私も負けないように走りこんで体力つけないと!

Expand opportunity to accessing new building blocks

Building Block(BB) is key part of medicinal chemistry. Advances in science medicinal chemists can have opportunity to access novel BBs and they do not consider how to make BBs these days. In my personal opinion, unique BB will be the strong point of the their company. So medchem need to pay a lot of effortContinue reading “Expand opportunity to accessing new building blocks”

Investigation of PAINS filter with pharmaceutical company data set

PAINS filter is well know molecular filter to remove promiscuous compounds for HTS. Many computational tools implement PAINS filter as a drug like filter. I also use the filter but I do not confirm the reliability with our in house dataset. Here is a report from researchers in Lilly about investigation of PAINS filter withContinue reading “Investigation of PAINS filter with pharmaceutical company data set”

Get 3D distance matrix with rdkit #RDKit

I updated rdkit of my env from 20180301 to 20180303 with anaconda. ;-) When I want to get 3D distance matrix of the molecule I use Get3DDistanceMatrix method. But I found that rdDistGeom.GetMoleculeBoundsMatrix returns almost same results. 3DDistance matrix is useful for feature of 3D QSAR. I would like to use these method. And alsoContinue reading “Get 3D distance matrix with rdkit #RDKit”