I’m medicinal chemist in mid-size pharmaceutical company in Japan.
I’m interested in chemoinformatics, CADD technology, statistics and programming.
My favorite programming language is Python and Javascript.
What I like is…. running, welsh corgi pembroke.

This blog post is my diary, memorandum or…..

14 thoughts on “About

  1. Hello, thank you for all your blog posts. they are very educative. Please, I have a request. Can you do a detailed post on how to develop Structure-Activity Similarity (SAS) maps using RDKit like the one that is plotted on this site: https://unam-shiny-difacquim.shinyapps.io/ActLSmaps/

    Please some explanation of the process will be very much appreciated

    Thank you!

  2. I’m interested if you can detail plans in the thought process in preparing small molecule data-sets. Like what to look out for and think about.

    Most papers just jump over it and give the full dataset and just the ML methods used.

    Your blog is AMAZING, thanks for the great content!

  3. Hi, I graduated as a bachelor of science in chemistry and interested in cheminformatics. Happy to find your blog via reddit & see that you are still active posting here. I hope you continue to succeed in your cheminformatics endeavor!

    May I ask some questions:
    To work / do research in cheminformatics field, what kind of study should I choose?
    Because there is not many degree that is directly titled as “cheminformatics”.
    Which one is more suitable:
    1. Bioinformatics
    2. Theoretical / computational chemistry
    3. Computer science – machine learning / data science
    4. Computer science – software engineering

    Also, what is the difference between computational chemistry and cheminformatics?
    I would really appreciate it if you have any online resource / tutorial to delve into cheminformatics that can be shared.

    Thank you in advance.

    • Congratulations on your graduation and thank you for your query!
      You have an interest in chemoinformatics that sounds nice. As same as you my background is organic chemistry(total synthesis of natural products).

      My opinion is below.

      1) The bioinformatics skill set is useful if you have an interest to biology it is nice timing for learning bioinformatics. If you can have skill about chemo/bio informatics it will be strong point of you.

      2) If you would like to learn more details of science, I recommend to learn theoretical/computational chemistry such as quantum chemistry. Because most of chemoinformatics approaches are pattern recognition I think.

      3-4) Recently there are many job opportunities of computer/data science. For these area, I think it is required wide range of skill set such as analysis, statistics, coding, data visualization, science, database handling etc.
      It is exciting area. technology changes very rapidly. ;)

      Difference of computer chemistry and chemoinformatics area of the world is covered I think. Computational chemistry has more wide meaning which uses computer for solving the chemistry issues.

      Any way the answer for the your question depends on things what you want to do.

      I am working in pharmaceutical company as medicinal chemist now. And I like programming so I am happy to use chemoinformatics in my project. You can try everything, enjoy!

      There are many online resource if you search on google. And I recommend check the Pat’s blog post. It is really useful.
      Any comments and questions are appreciated.

      • Thank you for the response!

        So from bioinformatics, computational chemistry, and computer science, which one is closer to cheminformatics?

        Can you tell me your background after organic chemistry, did you continue to a formal education to learn cheminformatics or you learn it from your job/by yourself?

        Thank you for Pat’s blog link. That is certainly very useful!

      • Hi,
        I think computational chemistry is similar to chemoinformatics.

        I graduated university, I joined current company as a medicinal chemist. And I learned and write code in my hobby ;) So I learned chemoinformatics by myself in my free time.
        I hope this would be answer for your questions.

      • Thank you for the answer iwatobipen. It is now clearer for me. For now, I will keep looking on the internet for cheminformatics resources.

        Best of luck with your chemistry career!

  4. Hi there,
    I saw that you tweeted about a recent ChemRxiv paper on strategic molecules for circular supply chains. I’m writing about the paper for Chemistry World magazine, published by the Royal Society of Chemistry, and am looking for someone with expertise in chemoinformatics to comment on the study. If you are interested, please send me an email or Twitter message (@chemistry_kat).

  5. Hi, the moleculardesigntoolkit demo seems very useful. Where/how did you find documentation to piece it together? Do you know of tutorials or examples for absorption spectra? Photoinduced absorption? Cation absorption? Thank you

  6. Hi @iwatobipen,

    My name is Ganesh and as a fellow Cheminformatics enthusiast, I really like your work.

    I am currently having a look at how to use the script in the your blog to calculate the SA score: https://iwatobipen.wordpress.com/2013/11/04/estimation-of-synthetic-accessibility-score/

    However, I do not understand what the input file should look like and the link to your dataset doesn’t seem to work.

    I was wondering if you could forward me the input file you used for the script? This would be very helpful


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