For academia, individuals, and companies

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From a bench-only researcherto a Wet × Dry researcher.

In silico drug discovery education program

VALUES

Values

MISSION

Increase the number of Wet × Dry researchers.

VISION

Remove the wall between experiment and computation, and nurture researchers who can generate their own research questions.

CHALLENGES

Does this sound familiar?

  • I want to make experiments more efficient.
  • I want to take on time-consuming, challenging topics — and still build a stronger publication record.
  • I want to keep doing research, even while other work keeps me busy.

ANOTHER PATH

Wet × Dry as a choice

Adding dry research and analysis to your own work can take the project up a stage.

01

Far more efficient experiments

Simulation reduces the number of trials and the risk of failure, so bench time goes to the checks that matter. Automating data analysis also makes the work more efficient.

02

Better use of time

Dry research runs on a PC, so you can do other work while calculations finish. AI helps with planning and coding, so you can set up conditions and run the most useful jobs.

03

A growing publication record

Because the computer does the work, dry research tends to deliver results faster than bench experiments. You can build output with dry research alone, or secure a publication record with it while settling into a challenging wet-lab topic.

STORY

How BaraPhaSilico began

During my PhD I was a wet-lab researcher. The more time I spent at the bench, the more I felt how long it takes to get even a single result.

Around me, others were struggling too, waiting for results that would not come. It was not a lack of effort. Experiments test hypotheses one by one, and that simply takes time.

After graduating I stepped away from drug discovery for a time, but the wish to keep working on it did not change. I taught myself in silico methods and used the computer to narrow hypotheses. With the help of my collaborators, I was able to write the work up as a paper about six months after starting the project.

Learning dry methods makes it possible to examine a hypothesis before going to the bench, and to look at experimental data from another angle. Dry work does not only support wet research; it can produce results of its own, and the range of what a researcher can do grows.

I wanted to bring this experience to researchers who, like me, were unsure how to move their work forward. That wish became BaraPhaSilico.

We understand the reality of experimental research, and from there we support data analysis, hands-on in silico drug discovery, and the learning of new techniques. We walk alongside researchers as they combine their own expertise with new methods and take the work forward.

By bringing AI and IT together with a broad view of drug discovery, we hope to shorten the time it takes to find a medicine, and to help one more medicine reach the people who need it.

FOUNDER

Founder

Koki Shinbara, founder of BaraPhaSilico

Koki Shimbara

新原 光貴

Founder, BaraPhaSilico / Ph.D. in Science / Bioinformatician at a global life-science company / Visiting faculty, Hokkaido University vaccine R&D hub

At Tokyo University of Science (Faculty of Pharmaceutical Sciences) and the University of Tokyo (Graduate School of Science), he worked on peptide screening, small-molecule chemistry, peptide synthesis and biochemical assays.

After graduating, he learned DX and IT at an IT startup, then worked as a bioinformatician at a global life-science instrument vendor.

Wanting wet-lab researchers to take up dry research, he founded BaraPhaSilico.

WORKFLOW

The in silico drug discovery program, step by step

From building a compound library through in silico screening and MD simulation to proposing final compounds. You go through the whole workflow, one that can lead to a publication with nothing but a PC, on your own research topic.

Workflow: library construction, in silico screening, MD simulation, final compound
  1. 1

    Compound library construction

    Design and filter a library of small molecules and/or peptides from public databases to fit your target.

  2. 2

    In silico screening

    Evaluate binding to the target protein computationally by docking and narrow down hit compounds.

  3. 3

    MD simulation

    Verify complex stability with molecular dynamics and estimate binding energies with MM/PBSA and related methods.

  4. 4

    Final compounds & publication

    Propose compounds after interaction analysis and ADMET evaluation, and write the paper.

Typical timeline

No programming experience

Learning
about 3 months
Publication
about 6 months

Programming experience

Learning
about 1.5 months
Publication
about 3 months

AFTERWARDS

After the program

Before

  • Candidates can only be found at the bench.
  • Unsure how dry results become a paper.
  • AI is something you have only heard about.
  • A bench-only researcher.

After

  • You run library construction, screening, MD and interaction analysis on your own topic.
  • You have a template for publication: figures, narrative and journal choice.
  • You can use the latest AI methods and know how to run research with AI.
  • A Wet × Dry researcher who narrows hypotheses computationally, tests them experimentally and sets the next question.

COMPARISON

Comparison with other services

BaraPhaSilicoGraduate schoolCoding bootcamp
FeesFrom JPY 20,000 per month (academia / individuals). Companies: JPY 300,000 lump sum.Hundreds of thousands to over JPY 1,000,000 per year.Hundreds of thousands of yen.
DurationFrom a few months; designed around your topic through to publication.Two years for a master’s, three or more for a PhD.A few months; ends when the curriculum ends.
PublicationMentoring through to publication on your own research topic.Publication on the lab’s topic; progress depends on your supervisor.Not covered. Research and publication are out of scope.
InstructorDirect mentoring by a PhD from the wet lab who taught himself in silico drug discovery and published.Your supervisor; the field depends on the lab.Software engineers; limited experience in drug discovery or research.

Descriptions of graduate school and bootcamps are typical examples.

Textbook

The Complete Guide to In Silico Drug Discovery: Write a Paper from Home

This is the textbook we teach from. It is updated regularly.

Read on Zenn (Japanese)

PROGRAM

Nine pillars of the mentoring program

We mentor you through the textbook, video lectures and weekly meetings, combining the following as needed.

01

Research environment setup

Linux/WSL, conda, GPU: we get the error-prone setup out of the way first.

02

Practical Python for researchers

Learn the Python you need by running analyses on your own data.

03

Literature review & hypothesis design

How to read papers, organise prior work and formulate testable hypotheses.

04

Hands-on in silico drug discovery

Actually run docking, virtual screening and MD simulations.

05

AI for research productivity

Safely bring generative AI into research, coding and writing.

06

Materials you can revisit anytime

Rewatch the video lessons as often as you need. The textbook code is maintained so it keeps running.

07

Publication strategy & study design

Journal selection, figure planning and reviewer response, planned from the start.

08

Code review & coding support

We review your code and help it grow into a reproducible analysis pipeline.

09

Unlimited questions & online discussion

Ask anytime on Discord, discuss regularly on Zoom. Less time stuck alone.

Founder's paper

Identification of KKL-35 as a Novel Carnosine Dipeptidase 2 (CNDP2) Inhibitor by In Silico Screening

Shinbara K. et al., Molecules 2025, 30(22), 4370.

Read the paper (Open Access)

What participants say

I had no background in bioinformatics, yet the basics of in silico screening of a small-molecule library against a target protein were explained in a way I could follow. I did not even know how to use a command line, and I hit error after error, but I still made it from setting up a virtual environment all the way to running an MD simulation. I owe that to my mentor and I am truly grateful.

The technical book was also updated with the points I stumbled on and with tools that were not covered when it was first written, which makes reviewing much easier (I look forward to further additions).

My own PC is probably not powerful enough to run MD simulations at full tilt, but this program has clearly lowered the barrier I felt towards bioinformatics. It has sparked a desire to understand the field more deeply; I intend to keep learning and build more practical skills, and if the chance arises I would very much like to be mentored again.

Postdoctoral researcher, M

My research had been centred on wet-lab experiments, so I was not very familiar with dry analysis or programming and felt some anxiety, but by actually working hands-on I learned a great deal.

Errors were frequent as I got used to Python, but each time I received careful guidance and was able to move forward while properly understanding every step. Gaining knowledge and intuition through practice, something you cannot get just by reading a book, was extremely valuable.

Because of my PC’s specifications I could not run the MD simulation myself and the actual calculation was run on my behalf, but I came to understand the workflow and its significance. The in silico screening also turned up compounds that could become the seed of a research project, a major outcome that I hope to carry through to a journal submission. Thank you for this valuable opportunity.

Assistant professor, H

PRICING

Pricing

Academia / individuals

MonthlyJPY 20,000

Lump sumJPY 120,000

(tax included)

  • Mentoring through to publication
Book a free first consultation

Companies

Lump sumJPY 300,000

(tax included)

  • Includes one month of technical advising after the program ends.
Book a free first consultation
  • When you publish, please credit us by name (for example as co-first author) according to our contribution to the research.
  • Please also provide a testimonial of about 300 Japanese characters at the end of the program.
  • The textbook is purchased separately.

FOR WHOM

Who it is for — and who it is not

A good fit

  • Master's and PhD students, postdocs, early-career PIs and industry researchers who seriously want to change how they do research
  • People who can commit 10+ hours per week and work hands-on
  • Wet-lab researchers who want to add computation to their toolkit
  • Anyone who wants to publish with in silico drug discovery or bioinformatics

Not a fit

  • Those looking to outsource analysis (this is not a contract-analysis service)
  • Those who cannot set aside time to do the work themselves
  • Those who only want quick results without learning

FAQ

Frequently asked questions

How is this different from your collaborative research service?

The mentoring program is built on the premise that you do the hands-on work. We explain concepts, review your code, help you get unstuck and discuss study design, but we do not run the analysis for you. In return, every skill and result you gain is yours. If you would rather have us carry out the analysis, please contact us about collaborative research instead.

Can I join with no programming experience?

Yes. Even if you have never used a command line, we start from environment setup and move one step at a time. Most past participants came from a wet-lab background.

What kind of computer do I need?

Docking and data analysis run on an ordinary laptop (Mac, or Windows with WSL). MD simulation is more comfortable with a GPU; if that is not available to you, we discuss options at the first consultation.

How much time is required?

The program is for people who can commit at least 10 hours per week. Duration and pace are designed together at the first consultation, based on your topic and goal (conference presentation, journal submission, etc.).

What is the difference between academia/individual and company fees?

Academia and individuals pay JPY 20,000 per month (or JPY 120,000 lump sum). Companies pay JPY 300,000 lump sum. The company plan includes one month of technical advising after the program. All fees are tax included.

Do you work in English?

Yes. Our founder has provided technical consulting to overseas researchers and can prepare materials and hold discussions in English.

CONTACT

Contact / free first consultation

Enquiries about the mentoring program, collaborative research and science marketing are welcome. We usually reply within 2–3 business days.