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 lastContinue reading “Look Back at 2021 #diary”
Tag Archives: diary
Cryo-EM data analysis with deep learning #arXiv
Recently number of publications with cryo-EM is growing. And also number of data storage is growing.From EMDB, http://www.ebi.ac.uk/pdbe/emdb/statistics_main.html/I could get following statistics. And now, Cryo-EM is collecting a lot of attention in drug discovery area because the method has possibility of determination for difficult targets that can not accessible to X-ray analysis. I’m not sureContinue reading “Cryo-EM data analysis with deep learning #arXiv”
明けましておめでとうございます
2019年に入りました。2018年後半の指骨折に始まり年末年始のインフルエンザ、インフルエンザ明けの謎の発熱＆咳からやっと復活しつつあります。健康の大切さを改めて痛感する年末年始となりました。また、抗インフルエンザ薬を飲み回復が早かったのを実感し、薬を作れる仕事に携われる事は改めて素晴らしいなと思った次第です。 まあ、今年は何はともあれ自己管理を徹底したいです。昨年は業務内容がガラッと変わり自分のやりたいことと、アサイメントが比較的同じベクトルになっていて自分にとって、とても良い年でした。ただチョット自分の興味に突っ込みすぎた部分もあり、もう少し創薬研究をどうやったら加速できるかという部分を強く意識していきたいと思います。また、昨年は出張が多い年でもあり、スケジュール管理の甘さが露呈しました今年はこの辺も意識しよう。 社会人になってから今までを振り返ると、分野のフロント行ってる方と議論できる機会を持てて恵まれてるなって思います。今年も、積極的に外にも目を向けたいなと思います。いやほんと周りはみんな優秀な方ばかりなので勉強たくさんできて感謝感謝です。 で、今年の目標1. Githubにもっとコードあげる Githubでコード管理しておくとあれなんだっけって時に振り返れていいですよね。ということで今まで以上にうまく利用したいと思います。2. 英語 まあコレはもう必須ですよね、、、海外出張行ってディスカッションするにも下手でもいいから話せないことにはなんともなりませんし、、、3. pytorch なんとなく使ったことはあるけどあまり深く勉強はしてなかったので今年はコレでなんか作りたいですね。今まで僕はTensorflowまたはKerasメインでしたので一度Define by runの方も触ってみようと思います4.数学 コレはまあ前からなんですが論文読んで自分で実装できるくらいの素養をつけたい。5.体調管理+体力作り！ 最近運動不足で10kmも走ると満足してしまうようになってしまったのでもう一度体鍛えてフルマラソンに挑戦したいですね。。。 つらつらと駄文を書いてしまいましたがまあ今年もぼちぼちやっていこうと思っています。いつも家でパソコンばっかりいじっている私を受け入れてくれる家族に感謝を述べて今日の投稿を終わりにしたいと思います。 皆様にとって今年が昨年以上に良い年になりますように！
Diary….
I like my town. This town is comfortable for me to live in, because it is not too urban like Tokyo or rural. There are many beautiful place and following pictures are my favorite place. The water in this river is very clean. I can see firefly in summer around here. I want to this sceneryContinue reading “Diary….”
Make Docker image File with Chemoinformatics toolkits.
Docker https://www.docker.com is an open platform for distributed applications for developers and sysadmins. Providing docker image that means every one build same environment easily. It’s means create own image and share image. Docker provide container. Containers running on a single machine all share the same OS kernel. It’s difference of normal VM. I used dockerContinue reading “Make Docker image File with Chemoinformatics toolkits.”
Visualizing the process of lead optimization
Some time we set milestones to management of portfolio, or/and to check the progeress of projects. These data were reported document, power point slides etc, so it’s difficult to grasp situation of LO timely. Researchers at GSK published a solution of visualize LO process. It was impressive for me. Link is here. http://www.ncbi.nlm.nih.gov/pubmed/26262898 They calledContinue reading “Visualizing the process of lead optimization”
Passport for compound.
I was interested in the title. “Compound Passport Service” http://dx.doi.org/10.1016/j.drudis.2015.06.011 AZ made passport for compound to manage compound rights tracking. The system can manage status of compounds, like ownership, permission and structure shared. I really impressed with the concept and system because I think that management of compound(and right) logistics is key factor in DrugContinue reading “Passport for compound.”
The result
I went to my old school the day before yesterday, I like my old school. An event about chemoinformatics was held here. I enjoyed presentation of all participants. My prediction result was …….(please don’t ask ;-)) All teams used two approaches SBDD or LBDD, and winner used LBDD approach. It’s worth to think about whichContinue reading “The result”
Think about SAR analysis.
I lost a chance of participation in RDKIT-UGM because ticket was sold out. ;-( I’ll try next year…. SAR analysis is key for drug discovery. MMPA is one of major tool, I like the method. Because MMPA is easy to check effect of substituent in molecule. But sometime, it difficult to understand why the parameterContinue reading “Think about SAR analysis.”
Importance of communication
I often think about how to Importance of communicate with bench chemist and computational chemist. Sometime, in my situation, communication tools are limited because of skills, tool license, or any other reasons. For example, comp. chemist presented us using MOE but bench chemists often use PyMol so data translation is required. And spotfire is difficultContinue reading “Importance of communication”
review for kinetics
I found nice review about kinetics of drug binding and residence time. http://www.ncbi.nlm.nih.gov/pubmed/25782745 To improve in vitro, in vivo potency, I some time try to get SKR for designing molecule. If I got correlation only residence time and lipophilicity or molecular weight, the information is not so good. Because too liphophilic or heavy molecule isContinue reading “review for kinetics”
Compound Library in Europe
I read a perspective in DDT today. The title was “The Joint European Compound Library: boosting precompetitive research”. Link is following url. http://www.sciencedirect.com/science/article/pii/S1359644614003419 The Joint European Compound Library (JECL) is a key component of the IMI European Lead Factory (ELF) and brings together over 321 000 high-quality, drug-like and lead-like compounds from the in-house collectionsContinue reading “Compound Library in Europe”
MPO about drug discovery
I have question about MPO multi-parameter optimisation in drug discovery. My opinion is that designed molecule’s biological activity and ADMET profile are not always correlate. So, to design molecules that has good profile, I think it is important to get data about molecules not only biological activity but also phys-chem and ADMET profile even ifContinue reading “MPO about drug discovery”
リニア鉄道館に行ってきました
先週の土曜日に、新幹線が好きな２歳の息子が喜ぶかと期待して行ってきました。 館内には現在、本格運用を目指し試験中のリニアモーターカーの旧モデルの展示があったり、原理の説明があったり、実は自分の方が興味津々で見たり聞いたりしていて、、 旧型のドクターイエローはかなり食いついていました。 またNゲージのジオラマもなかなか見事なもので、しばし見入っていました。 うちのあるのはプラレールなんですがNゲージにちょっと惹かれてみたら、、、 結構お高いですね〜あれだけのものを作るには場所と予算が、（笑） 一日過ごせて、親子で楽しんだので良いお出かけになりました。 今度はもう少し分かるようになってからまた行きたいなぁ。
Is life worth living? 