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

ABOUT

Hello, I'm Bundit, a Ph.D. student in Information Science and Technology at 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

" SUCCESS DOES NOT COME FROM SMARTNESS

BUT IT'S CAUSED BY THE IMPLEMENTATION. "

MY ACHIEVEMENTS

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  • 2022

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

  • 2022

    Research Advisor for High School Students and Received Top Award, First Award, and Second Award of Thailand in Interdisciplinary Fields (Computational Biology & Bioinformatics), Young Scientist Competition (YSC) 2022

  • 2021

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

  • 2021

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

  • 2020

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

  • 2018

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

  • 2015

    Academic Activist and Person who made 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

  • 2013

    Intermediate level (Band 4 of 6) in the PSU English Test

  • 2012

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

  • 2008 – 2010

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

EXPERIENCES

Next Invited Talks

Recent Invited Talks

  • Talk 76 – Jump-start Science Project & Scientist Invents Dough

    Jump Start Science Camp for Grade 10 students of Samutsakhonburana School

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

Outstanding Extracurricular Activities

  • Regeneron International Science and Engineering Fair 2022 (Regeneron ISEF 2022)

    Thai Interpreter

    Year: 2022

  • 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.

    Co-founder

    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

    Organizer

    Year: 2015

Research Experience

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

    Research Experience at NSTDA, Thailand (JSTP Scholarship)

    Mentors: Assoc. 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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RESEARCH INTERESTS

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, integrated with computational techniques such as Machine Learning, Deep Learning, Computational Biology, and Computational Chemistry.

Current research domains are included as follows:

  • Molecular Property & Interaction

    focuses on the relationship of biomolecular 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 designing and developing model architectures and feature engineering strategies to improve predictive performance for machine learning and deep learning models.

Current Projects

  • Developing deep learning model architecture for bioactivity prediction (i.e., receptor tyrosine kinases, HIV protease, and HCV protease)

  • Developing deep learning model architecture for cancer drug response prediction using multi-omics data

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.

  • Briefings in Bioinformatics, Oxford University Press

  • Nucleic Acids Research, Oxford University Press

RESEARCH ADVISEMENT

Students: 1. Tisorn Naphattalung, 2. Matin Kositchutima, 3. Kittiphat Pongarunotai
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2022

Students: 1. Tisorn Naphattalung, 2. Surapa Panjaphakdee, 3. Matin Kositchutima
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Pawit Kaewnuratchadasorn, 2. Wutthipong Chongchareansanti, 3. Nattawin Yamprasert
Advisors: Dr. Sarote Boonseng and Bundit Boonyarit
School: Mahidol Wittayanusorn School (MWIT)
Year: 2021 – 2022

Students: 1. Thiranich Sawatdipap, 2. Phanfa Laohasinnuruk
Advisors: Dr. Tanawan Leeboonngam and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Theeradon Sakpetch, 2. Phandej Soisamuth
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Parajaree Ungudonpakdee, 2. Thanasan Kumdee
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Theeradon Sakpetch, 2. Phandej Soisamuth
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Natthakan Saeng-nil, 2. Puri Virakarin
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Natthakan Saeng-nil, 2. Puri Virakarin
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2019 – 2020

Students: 1. Chawapon Tritipchatsakun, 2. Thanis Prucksikanont
Advisors: Pimsiri Danphitsanuparn and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2018 – 2019

BioXcepTion

BioXcepTion is a high school 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)

PERSONAL

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.

CONTACT

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