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Biomolecular Artificial Intelligence & Digital Biology

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Computational Structural Biology & Machine Learning for Biomolecules

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Molecular Machine Learning & Chemoinformatics for Drug Discovery

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Computational Structure-based Drug Discovery

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Molecular Modeling & Molecular Dynamics Simulation for 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.

" SUCCESS DOES NOT COME FROM SMARTNESS

BUT IT'S CAUSED BY THE IMPLEMENTATION. "

MY ACHIEVEMENTS

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2023
JSTP Mentor for High School Student and Received Long-term Scholarship, National Science and Technology Development Agency (NSTDA)
2023
Research Advisor for Genius Olympiad Finalists and Received Honorable Mention Award in Science, Genius Olympiad 2023
2023
Research Advisor for ISEF Finalists and Received Fourth Place Award in Computational Biology and Bioinformatics, Regeneron ISEF 2023
2023
Research Advisor for High School Students and Received Top Award and First Award of Thailand in Interdisciplinary Fields (Computational Biology & Bioinformatics), and Second Award of Thailand in Computer Science, Young Scientist Competition (YSC) 2023
2022
Research Advisor for Genius Olympiad Finalists and Received Bronze Medal in Science, Genius Olympiad 2022
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 Genius Olympiad Finalists and Received Gold Medal in Science, Genius Olympiad 2021
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

Recent Invited Talks

Talk 94 – Paperwork, Project Display and Project Materials Preparation & Effective Design for Project Display, Quad Chart, and Project Presentation
for Regeneron ISEF 2024 Finalists (Fair: Young Scientist Competition (YSC), THA002)
Organized by National Science and Technology Development Agency (NSTDA)

Venue: Sirindhorn Science Home, Science Park, Pathum Thani and Siam Commercial Bank Training Center (Tawanron Beach), Chonburi
Date: Mar 17-19, 2024

Talk 93 – Science Project Commentator and Committee in Final Round (Committee for Special Awards)
The Twenty-Sixth Young Scientist Competition (YSC 2024)
Organized by National Science and Technology Development Agency (NSTDA)

Venue: Sirindhorn Science Home, Thailand Science Park, Pathum Thani
Date: Mar 2-3, 2024

Talk 92 – Improving Research Report and Quad Chart Camp
for teachers and high school students who have been selected as representatives to participate in the GENIUS Olympiad
The network level of Enrichment Program of Science, Mathematics, Technology and Environment (SMTE)
Organized by National Science and Technology Development Agency (NSTDA) and Office of the Basic Education Commission (OBEC)

Venue: Sirindhorn Science Home, Thailand Science Park, Pathum Thani
Date: Feb 24-25, 2024

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, aiming to advance the understanding of biomolecular science for innovative and industrial applications. The main research integrates relevant knowledge from Biochemistry, Chemistry, Pharmaceutical Sciences, and Computer Science, employing computational techniques such as machine learning, deep learning, computational biology, and computational chemistry.

The current research themes, collectively termed “CompBio3D – Computational Biomolecular Discovery, Design, and Development”, encompass the following areas:

Molecular Property & Interaction
focuses on elucidating the relationship of biomolecular structure, leading to molecular properties and interactions predictions.
Molecular Design & Discovery
focuses on the structural analysis of biomolecules to facilitate the discovery, design, and understanding of molecular phenomena.
Molecular Representation & Learning
focuses on the design and development of model architectures and feature engineering strategies, enhancing the predictive performance of machine learning and deep learning models in biomolecular science.

Current Projects

Machine Learning and Computer for Drug Design and Discovery:
(1) Tyrosine kinases
Machine Learning for Cancers Prediction and Diagnosis based-on Multi-omics Data:
(1) Cancers Drug Response
(2) Cancer Driver Genes and Biomarkers
Computational Biology and Machine Learning for Protein Structure Analysis:
(1) Chitin degradation proteins
(2) Asgard archaea proteins

Research Publications

Phengsakun, G., Boonyarit, B., Rungrotmongkol, T., & Suginta, W. (2023). Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: classical and machine learning scoring functions, and molecular dynamics simulations. Computational Biology and Chemistry, 107856.
Phengsakun, G., Boonyarit, B., & Suginta, W. (2021). 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. & 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.

Research Collaborations

Prof. Dr. Wipa Suginta
School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong, Thailand
Prof. Robert (Bob) Charles Robinson
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong, Thailand
- Research Institute of Interdisciplinary Science, Okayama University, Japan
Assoc. Prof. Dr. Thanyada Rungrotmongkol
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathum Wan, Bangkok, Thailand

RESEARCH ADVISEMENT

Machine Learning Assisted Biomarker Discovery for Lung Cancer Diagnosis Based on Multi-omics Data

Students: 1. Panuwat Wongpattanawut, 2. Phurivet Methmaolee
Advisors: Theerawut Chantapan and Bundit Boonyarit
School: Princess Chulabhorn Science High School Mukdahan
Year: 2022

Enhancing Deep Learning Model Toward Predicting Synergistic Cancer Drug Combinations Based on Drug Structures and Multi-omics

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

Machine Learning Enables Enzyme Kinetics Prediction of Glycosidases Based on Molecular Descriptors and Physicochemical Properties

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

Hybrid Graph Attention Networks Toward Cancer Drug Response Prediction using Chemical Structure and Multi-omics

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

Data Analysis of Effective Ligands to Inhibit the Activity of P2Y12 Leads to Drug Discovery and Design for Thromboembolic Treatment

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

Semi-supervised Learning with Graph Neural Networks for Drug Response Prediction Leads Discovery of HIV Inhibitors

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

Deep Transfer Learning-Based Hit Compound Classification for Heart Failure Drug Discovery on Small Datasets

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

An Integrated Multi-task Learning and Transfer Learning-based Approach for Structure-Property Leads Drug Discovery for HIV and HCV Protease Inhibitors

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

EGFRNet: Transfer and Multi-task Learning Based on Graph Convolutional Network Toward Multi-target Drug Discovery Against Cancers for EGFR-Family Proteins

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

Application of Machine Learning Technique Assisted Bioactivity Prediction of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR

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

Computational Analysis of Glucagon Receptor (GCGR) and Antagonists Structure for Screening Anti-Diabetics Compounds

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]

Natural Language Processing and Representation Learning Lab (NRL)
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