Integrative Computational Structural Biology and Machine Learning
Molecular Machine Learning for Drug Discovery and Enzyme Engineering
Computational Structure-based Drug Discovery
Molecular Dynamics Simulations of Biomolecules


Hello, I'm Bundit, Ph.D. student in Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand. I received a B.Sc. degree in Chemistry from Prince of Songkla University, Thailand and an M.S. degree in Biochemistry from Kasetsart University, Thailand.

Bundit Boonyarit




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  • 2021-2022

    Research Advisor for ISEF Finalists and Received First Place Award in Computational Biology and Bioinformatics, Regeneron ISEF 2021 & 2022

  • 2022

    Research Advisor for High School Students and Received Top Award, First Award, and Second Award of Thailand in Interdisciplinary Fields (Comp. Bio & Bioinfor), Young Scientist Competition (YSC) 2022

  • 2020-2021

    Research Advisor for High School Students and Received Championship of Thailand in Computer Science, Young Scientist Competition (YSC) 2020-2021

  • 2018

    Ph.D. scholarship from Vidyasirimedhi Institute of Science and Technology and PTT Group, and SCB

  • 2015

    Academic Activist and Person who make reputation for Faculty of Science, Prince of Songkla University, Hatyai Campus, Thailand

  • 2015

    Young Thai Science Ambassador 2014, National Science Museum, Thailand

  • 2014

    The 11th True Young Webmaster Camp

  • 2012

    JSTP scholarship student, National Science and Technology Development Agency, Thailand

  • 2008 – 2010

    Computer Olympiad Camp (POSN), 1st & 2nd camps, Walailak University, Thailand


Next Invited Talks

  • Talk 63 – Jump-start Science Project

    First Step to Become a Scientist Camp (Grade 10) for Demonstration School, University of Phayao

    Organized by National Science and Technology Development Agency (NSTDA)
    Date: May 26, 2022

Recent Invited Talks

  • Talk 62 – Food Crime Detection

    Fun Thinking With Science Around You Camps (Grade 7-8)

    Organized by National Science and Technology Development Agency (NSTDA)
    Date: Apr 26, 2022

Outstanding Extracurricular Activities

  • Thailand Machine Learning for Chemistry Competition (TMLCC)

    Organizer and Speaker

    Lecture: Machine Learning for Molecular Chemistry in a Nutshell
    Year: 2021

  • The White Room Enterprise Co., Ltd.


    Science camps for students interested in science and education and charity camps for students underprivileged in science education
    Year: 2012 – Present

  • 12th Young Webmaster Camp, Thailand Webmaster Association


    Year: 2015

Research Experiences

  • Computational Screening of Tripeptides Against Kinase-Domain for Human Epidermal Growth Factor Receptor 2 (HER2)

    Research Experience at NSTDA, Thailand (JSTP Scholarship)

    Mentors: Prof. Dr. Kiattawee Choowongkomon, Dr. Sissades Tongsima
    Year: 2014 – 2017

  • Characterization of Gelatin From Silver Carp Skin As Influenced by Acid Pretreatment

    Research Experience at Fac. Agro-Industry, PSU, Thailand (JSTP Scholarship)

    Mentor: Prof. Dr. Soottawat Benjakul
    Year: 2011 – 2012

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The research focus lies in Molecular Property & Interaction, Molecular Design & Discovery, and Molecular Representation & Learning with the goal of developing and leading to the understanding of molecular science knowledge that can be developed for innovation and industry applications. The main research employs knowledge relevant to Biochemistry & Molecular Biology, Chemistry, Pharmaceutical Sciences, and Computer Science, together with computational techniques such as Machine Learning, Deep Learning, Computational Biology, and Computational Chemistry.

  • Molecular Property & Interaction

    focuses on the relationship of biomolecules structure, leading to predict molecular properties and interactions.

  • Molecular Design & Discovery

    focuses on the structure of molecules and biomolecules, with the goal of discovering, designing, and understanding of molecular phenomena.

  • Molecular Representation & Learning

    focuses on the designing and developing model architectures and feature engineering strategies that result in enhanced prediction in machine learning and deep learning processes.

Current Projects

  • Deep learning for bioactivity prediction assisted drug discovery (Receptor Tyrosine Kinases, HIV, and HCV)

  • Deep learning for predicting enzyme kinetics (Glycoside hydrolase)

  • Machine learning model for precision oncology (drug sensitivity)

  • Machine learning-based scoring function for drug discovery (Receptor Tyrosine Kinases)

Research Publications

  • Phengsakun G., Boonyarit B., Suginta W., Docking-based virtual screening and pharmacophore analysis of novel GH-20 β-N-acetylglucosaminidase inhibitors. 7th International Conference on Biochemistry and Molecular Biology (BMB2021).

  • Virakarin, P., Saengnil, N., Boonyarit, B., Kinchagawat, J., Laotaew, R., Saeteng, T., Nilsu, T., Suvannang, N., Rungrotmongkol, T. and Nutanong, S., (2020). LigEGFR: Spatial graph embedding and molecular descriptors assisted bioactivity prediction of ligand molecules for epidermal growth factor receptor on a cell line-based dataset. bioRxiv.

  • Seetaha, S., Boonyarit, B., Tongsima, S., Songtawee, N., & Choowongkomon, K. (2020). Potential tripeptides against the tyrosine kinase domain of human epidermal growth factor receptor (HER) 2 through computational and kinase assay approaches. Journal of Molecular Graphics and Modelling, 97, 107564.

  • Boonyarit B, Mokmak W, Tongsima S, Choowongkomon K. (2016). Computational screening of tripeptides against kinase-domain for human epidermal growth factor receptor 2 (HER2). The 42nd Congress on Science and Technology of Thailand (STT42), 495-504.

Peer Review

  • Journal of Biomolecular Structure and Dynamics, Taylor and Francis Ltd. (IF = 3.310 (2018))

  • Briefings in Bioinformatics, Oxford University Press (IF = 11.622 (2020))

  • Nucleic Acids Research, Oxford University Press (IF = 16.971 (2020))


Students: 1. Tisorn Naphattalung, 2. Surapa Panjaphakdee, 3. Matin Kositchutima
Co-advisor: Dr. Thanasan Nilsu
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – Present

Students: 1. Pawit Kaewnuratchadasorn, 2. Wutthipong Chongchareansanti, 3. Nattawin Yamprasert
Co-advisor: Dr. Sarote Boonseng
School: Mahidol Wittayanusorn School (MWIT)
Year: 2021 – Present

Students: 1. Theeradon Sakpetch, 2. Phandej Soisamuth
Co-advisor: Dr. Thanasan Nilsu
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – Present

Students: 1. Thiranich Sawatdipap, 2. Phanfa Laohasinnuruk
Co-advisor: Dr. Tanawan Leeboonngam
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021

Students: 1. Parajaree Ungudonpakdee, 2. Thanasan Kumdee
Co-advisor: Dr. Thanasan Nilsu
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Natthakan Saeng-nil, 2. Puri Virakarin
Co-advisor: Dr. Thanasan Nilsu
School: Kamnoetvidya Science Academy (KVIS)
Year: 2019 – 2021

Students: 1. Chawapon Tritipchatsakun, 2. Thanis Prucksikanont
Co-advisor: Pimsiri Danphitsanuparn
School: Kamnoetvidya Science Academy (KVIS)
Year: 2018 – 2019


BioXcepTion is a KVIS student research team with a particular emphasis on Computational Biology, Computational Chemistry, and Artificial Intelligence.

(Click arrow for more information about our student research team)


I also have other interests including graphics design, presentation design, web design, online learning design, and server administration.

Graphics & Presentation Design

I have been interested in graphics and presentation design since I was an undergraduate student. I am most good a PR media design such as posters, brochures, and book covers. I have also been invited to lecture on the design for research presentation to school students and researchers.

Online Learning Design

I got an excellent chance from the Department of Chemistry, Faculty of Science Chulalongkorn University to build online learning for  Stereochemistry Lecture Series. This lesson is used in organic chemistry classes for undergraduate students. The instructional material includes videos and interactive activities.

Server Administration

I also have been interested in server administration for computational science research. In basic, I have used CentOS operating system and Slurm job scheduler for operation and management. For more detail, you can visit my GitHub for the setup instruction.


Bundit Boonyarit
Email: [email protected]

Scalable Data Systems Lab (SCADS)
School of Information Science and Technology (IST)
Vidyasirimedhi Institute of Science and Technology (VISTEC)

555 Moo 1, Pa Yup Nai, Wang Chan, Rayong 21210, THAILAND