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Biomolecular Artificial Intelligence & Digital Biochemistry

BAID RESEARCH BACKGROUND

The accelerating convergence of artificial intelligence with biomolecular science and biomedicine presents an urgent opportunity to generate meaningful, actionable insights at the molecular scale. At the Biomolecular Artificial Intelligence & Digital Biochemistry (BAID) team, we sit at the intersection of biochemistry, molecular biology, chemistry, pharmaceutical sciences, and computer science. We aim to develop computationally efficient and scalable frameworks for molecular deep learning, machine learning, and representation learning. In parallel, we apply modern computational and state-of-the-art techniques, including molecular docking and molecular dynamics simulation, to decode complex molecular phenomena. Our research tackles persistent challenges in biomedicine and biomolecular science, such as the inefficiencies of drug discovery pipelines (both low- and high-throughput), limited mechanistic understanding of molecular function, and data scarcity for therapeutic target identification.

Our work spans three interconnected research lines: (I) Molecular Representation Learning & Computations, (II) Molecular Discovery & Design, and (III) Molecular Modeling & Simulation. Together, these pillars enable us to build end-to-end pipelines that integrate data analysis, prediction, design, and simulation. Through this integrative and translational approach, we intend to conduct transformative research with real-world biomedical impact—pushing the frontiers of precision medicine, structural biology, and computational methodology.

We appreciate the funding and support from

Our mission is to transform the dynamic landscapes of biomolecular science and biomedicine by discovering, designing, and developing advanced AI models and computational frameworks, striding toward real-world impacts and accelerated scientific discoveries at the molecular scale.

RECENT NEWS

  • 2025

    Bundit Boonyarit – Received the ThaiSC (NSTDA) Voucher Program 3 award (as recipient) under the AI Research Project Grant Category for High Performance Computing (HPC) Credits valued up to 355,500 Baht (23,700 SHr) [PI: Assoc. Prof. Dr. Thanyada Rungrotmongkol]

  • 2025

    Parichamol Tantisuphakornsakul and Punnapa Pobsirikasem – Received Gold Medal in Science Project Competition for Senior High School Level (Biological Science Category) from The 42nd National Science Week, Eastern Region at Burapha University

  • 2025

    Punnapa Pobsirikasem – Received Outstanding Poster Presentation Award (Undergrad & High School) from The 19th International Symposium of the Protein Society of Thailand (PST2025)

  • 2025

    Parichamol Tantisuphakornsakul – Received Second Prize in Best Poster Presentation Award (Undergrad & High School) from The 19th International Symposium of the Protein Society of Thailand (PST2025)

  • 2025

    Parichamol Tantisuphakornsakul – Received Grand Prize, nominated by South Korea’s Ministry of Science and ICT) from Korea Science Academy Science Fair 2025 (KSASF 2025)

  • 2025

    Bundit Boonyarit – Received the ThaiSC (NSTDA) Voucher Program 2 award (as recipient) under the Research Project Budget Supplement Category for High Performance Computing (HPC) Credits valued up to 99,900 Baht (6,600 SHr) [PI: Assoc. Prof. Dr. Thanyada Rungrotmongkol]

  • 2025

    Bundit Boonyarit – Received VISTEC Honors for Outstanding Achievements that Brought Recognition to the Institute (Apr 2024 – Mar 2025)

BAID RESEARCH

The research focuses on discovering, designing, and developing computational frameworks and ML/DL models by integrating cutting-edge AI and computational approaches, striding forward in advancing both fundamental understanding and translational applications across biomolecular science and biomedicine.

The current research lines encompass the following areas:

  • Molecular Representation Learning & Computations

    Designs and develops computational frameworks and models to represent and interpret complex molecular and biological data.

  • Molecular Discovery & Design

    Discovers and designs novel therapeutic and biological molecules to specific biological activities and targets.

  • Molecular Modeling & Simulation

    Simulates and models the structure, dynamics, and interactions of biomolecules to uncover molecular mechanisms and functions.

Research Interests

Computational Biomolecular Design and Discovery

Biomolecular Machine Learning

Computer-aided Drug Discovery & Design

Computational Chemistry & Biology

Structural Bioinformatics

Current Research Lines & Projects

Research Line I: Molecular Representation Learning & Computations

Track I: Drug Discovery & Development

  • Molecular Representation Learning for Anticancer Drug Discovery Targeting Kinase Proteins

    Develops advanced molecular representation learning techniques for deep learning models (e.g., graph neural networks) to improve property prediction and interpretation in anticancer drug development against kinase protein targets.

  • Multimodal Deep Learning Based on Multi-Omics for Cancer Drug Response Prediction

    Designs and develops multimodal deep learning architectures that integrate multi-omics data (e.g., genomics, transcriptomics, and proteomics) to predict cell-line-specific cancer drug responses, including monotherapy and combination therapy, advancing personalized and precision medicine.

  • Explainable AI-Driven Adverse Drug Reactions Prediction Toward Pediatric Drug Discovery & Development

    Develops an explainable AI model to predict adverse drug reactions in pediatric drug development by integrating chemical, pharmacological, and biological data, along with physics- and chemistry-based features. This approach accelerates the development of safer pediatric drugs, improves health outcomes, reduces ADR incidence, and supports child-specific therapeutic strategies.
    (in collaboration with Dr. Rossukon Kaewkhaw, Fac. Medicine Ramathibodi Hospital, Mahidol University)

Research Line II: Molecular Discovery & Design

Track I: Enzyme Engineering

  • Computational Enzyme Engineering to Enhance DeHa2 Efficiency for Fluorinated and Chlorinated Organohalogen Degradation

    Leverages integrated deep learning and molecular dynamics simulations to predict potentially efficient DeHa2 variants (haloacid dehalogenase) and analyze the geometry and interactions of the binding pocket under real-world conditions, aimed at enhancing the degradation of toxic fluorinated and chlorinated organohalogen compounds.
    (in collaboration with T. Arjaree Thirach, KVIS, and Dr. Chayasith Uttamapinant, School of Biomolecular Science and Engineering, VISTEC)

Track II: Drug Discovery & Development

  • Computational Discovery and Design of Novel Small Molecules Targeting Glypican-3 for Liver Cancer Therapeutic

    Leverages molecular docking and molecular dynamics simulations to discover, design, and optimize therapeutic small molecules aimed at enhancing bioactivity and targeting glypican-3 in liver cancer.
    (in collaboration with Dr. Chayanon Ngambenjawong, School of Biomolecular Science and Engineering, VISTEC)

Research Line III: Molecular Modeling & Simulation

Track I: Structural Biology

  • Computational Structural Biology of Ascard Archaea Proteins: Exploring Structure-Function Relationships and Evolutionary Conservation

    Leverages deep learning and molecular dynamics simulations to investigate the structure-function relationships of eukaryotic-like protein homologs in Asgard archaea. These integrated methods aim to uncover the evolutionary connections between archaeal and eukaryotic protein machineries, identifying conserved fundamental interactions that have persisted across evolution.
    (in collaboration with Prof. Robert (Bob) Charles Robinson, School of Biomolecular Science and Engineering, VISTEC)

GRANTS & AWARDS

Research Grants

  • ThaiSC (NSTDA) Voucher Program 3 Award – AI Research Project Grant (2025)

    for high performance computing (HPC) credits valued up to 355,500 Baht (23,700 SHr) under the project "CanDrugAI: End-to-End AI-Driven Anticancer Drug Discovery & Development" [PI: Assoc. Prof. Dr. Thanyada Rungrotmongkol, Fac. Science, Chulalongkorn University]

  • ThaiSC (NSTDA) Voucher Program 2 Award – Research Project Budget Supplement (2025)

    for high performance computing (HPC) credits valued up to 99,900 Baht (6,600 SHr) under the project "CanDrugAI: End-to-End AI-Driven Anticancer Drug Discovery & Development" [PI: Assoc. Prof. Dr. Thanyada Rungrotmongkol, Fac. Science, Chulalongkorn University]

  • CanDrugAI: End-to-End AI-Driven Anticancer Drug Discovery & Development (2025–2027)

    Role: Co-PI | Sponsored by: National Science Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation (PMU-B), Thailand | Grant Number: B38G680006 [PI: Assoc. Prof. Dr. Thanyada Rungrotmongkol, Fac. Science, Chulalongkorn University]

Research Awards

  • Silver Medal in Science Project Competition for Senior High School Level (Biological Science Category)

    Venue: Thailand Young Scientist Festival (TYSF 21), Burapha University
    Awardee: Parichamol Tantisuphakornsakul and Punnapa Pobsirikasem
    Project Title: Enhanced DeHa2 for Organohalogens Degradation in Water through Deep Learning and Molecular Dynamics Simulation
    Received Date: 4 Nov, 2025

  • Outstanding Poster Presentation Award (Undergrad & High School)

    Venue: The 19th International Symposium of the Protein Society of Thailand (PST2025)
    Awardee: Punnapa Pobsirikasem
    Project Title: A Computational Framework for Engineering DeHa2 to Improve PFACs Degradation Efficiency
    Received Date: 9 Jul, 2025

  • Second Prize in Best Poster Presentation Award (Undergrad & High School)

    Venue: The 19th International Symposium of the Protein Society of Thailand (PST2025)
    Awardee: Parichamol Tantisuphakornsakul
    Project Title: Enhanced DeHa2 for PFACs Degradation Efficiency through Deep Learning and Molecular Dynamics Simulation Approaches
    Received Date: 9 Jul, 2025

  • Grand Prize (nominated by South Korea’s Ministry of Science and ICT)

    Venue: Korea Science Academy Science Fair 2025 (KSASF 2025)
    Awardee: Parichamol Tantisuphakornsakul
    Project Title: Enhanced DeHa2 for PFACs Degradation in Water through Deep Learning and Molecular Dynamics Simulation Methods
    Received Date: 4 Jul, 2025

  • VISTEC Honors for Outstanding Achievements that Brought Recognition to the Institute (Apr 2024 – Mar 2025)

    Venue: Vidyasirimedhi Institute of Science and Technology (VISTEC)
    Awardee: Bundit Boonyarit
    Received Date: 2 Apr, 2025

  • Best Oral Presentation in Computational Biology Session

    Venue: The 27th International Annual Symposium on Computational Science and Engineering (ANSCSE27)
    Awardee: Bundit Boonyarit
    Project Title: SynProtX: Artificial Intelligence Toward Enhanced Prediction of Synergistic Cancer Drug Combinations Using Large-Scale Protein Expression Profiling
    Received Date: 2 Aug, 2024

RESEARCH PUBLICATIONS

Recent Publications

The structure of an actin nucleus stabilized by villin

Robinson RC, Chongrungreang T, Ponlachantra K, Boonyarit B, Dilly GF, Li YI, Girguis PR, Copley RR, & Claridge-Chang A. (2025). Science Advances, 11(49), eadw6915.

Enhanced DeHa2 for PFACs Degradation Efficiency through Deep Learning and Molecular Dynamics Simulation Approaches

Tantisuphakornsakul P, Pobsirikasem P, Thirach A, Sirisakwisut P, Uttamapinant C, & Boonyarit B. (2025). The 19th International Symposium of the Protein Society of Thailand (PST2025), 113-125.

SynProtX: A Large-Scale Proteomics-Based Deep Learning Model for Predicting Synergistic Anticancer Drug Combinations

Boonyarit B, Kositchutima M, Phattalung TN, Yamprasert N, Thuwajit C, Rungrotmongkol T, & Nutanong S. (2025). GigaScience, 14, giaf080.

GraphEGFR: Multi-task and Transfer Learning Based on Molecular Graph Attention Mechanism and Fingerprints Improving Inhibitor Bioactivity Prediction for EGFR Family Proteins on Data Scarcity

Boonyarit B, Yamprasert N, Kaewnuratchadasorn P, Kinchagawat J, Prommin C, Rungrotmongkol T, & Nutanong S. (2024). Journal of Computational Chemistry, 45(23), 2001-2023.

RESEARCH TEAM

Current Members

Bundit (Aon) Boonyarit

Ph.D. Student

M.S. (Biochemistry), Kasetsart University, TH
B.Sc. (Chemistry), Prince of Songkla University, TH

Thanyathorn (Ton) Kingrat

Full-time Research Assistant

B.Eng. (Computer Engineering), Mae Fah Luang University, TH

Nopsinth (Will) Vithayapalert

Part-time Research Assistant

M.S. (Computational Finance, Management Science and Engineering), Stanford University, USA

B.S. (Operation Research, Management Science and Engineering), Stanford University, USA

Nattawin (Natt) Yamprasert

Part-time Research Assistant

Undergraduate Student in Computer Engineering, Sirindhorn International Institute of Technology (SIIT), Thammasat University, TH

Parichamol (Prachan) Tantisuphakornsakul

Student Researcher

High School Student, Kamnoetvidya Science Academy (KVIS), TH

(in collaboration with T. Arjaree Thirach and Dr. Chayasith Uttamapinant)

Punnapa (Ming) Pobsirikasem

Student Researcher

High School Student, Kamnoetvidya Science Academy (KVIS), TH

(in collaboration with T. Arjaree Thirach and Dr. Chayasith Uttamapinant)

Former Member

Krong (Ton) Krongyuth

Research Intern

B.Sc. (Mathematics), Mahidol University, TH

POSITION OPENINGS

We welcome undergraduate interns who are eager to push the boundaries of knowledge in interdisciplinary and computational sciences, advancing the fields of biochemical, biomolecular, biomedical, pharmaceutical sciences through integrative AI and computational approaches.

Eligibility:

  • Track I – ML/DL for Drug & Therapeutic Target Discovery:
    – An undergraduate student (≥ Year 2) with a strong academic record (GPAX ≥ 3.25/4.00)
    in one of the following or related fields: Computer Science, Computer Engineering, Biomedical Engineering, Mathematics, Statistics, Machine Learning, Data Science, or Computational Sciences.
    – Hands-on experience with Python programming and familiarity with ML/DL toolkits (e.g., TensorFlow, PyTorch).
    Understanding of ML/DL fundamentals, with an interest in applying advanced techniques to biomolecular science and/or translational medicine/pharmaceutical science problems.

     

  • Track II – Computational Biology for Drug Discovery & Structural Biology:
    – An undergraduate student (≥ Year 2) with a strong academic record (GPAX ≥ 3.25/4.00) in one of the following or related fields: Computational Biology, Bioinformatics, Biomolecular Science, Bioengineering, Biomedical Engineering, Biochemistry, or Molecular Biology.
    – Hands-on experience with computational biophysics/structural biology techniques and software, including molecular dynamics simulation, molecular docking, and/or molecular visualization (e.g., AMBER, GROMACS, GOLD, PHENIX, Coot, PyMOL, Chimera, Rosetta, etc.).
    – Understanding of structural biology and bioinformatics fundamentals, with an interest in applying advanced techniques to biomolecular science and/or translational medicine/pharmaceutical science problems.

     

  • Highly motivated, adaptable, and passionate about interdisciplinary and computational sciences research.
  • Availability for a full-time internship of at least 3 months or more.
  • Bonus: Proven track record of achievement in specialized activities related to computer science, computational science, or artificial intelligence.


How to Apply?:

To apply, please introduce yourself and submit the following documents (in either Thai or English) to Bundit Boonyarit via email at [email protected] or [email protected]:

  1. CV
  2. Academic Record
  3. Certificates or Records of Achievements
  4. Statement of Interest (Cover Letter)
  5. Supporting Document(s) (if any)


Selection Process:

The candidate will receive an email confirmation regarding the final selection process, which consists of two stages: (1) an assignment and (2) an interview.

If you are interested or have any queries, please feel free to reach out to [email protected] or [email protected]

RESEARCH COLLABORATIONS

Domestic Collaborations

  • School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand

  • Faculty of Science, Chulalongkorn University, Thailand

  • Chakri Naruebodindra Medical Institute (CNMI), Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand

  • Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand

  • Faculty of Engineering, Khon Kaen University, Thailand

International Collaborations

  • Research Institute for Interdisciplinary Science (RIIS), Okayama University, Japan

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)

ACADEMIC SOFTWARE

Our group is committed to developing open-source academic software and curated datasets that drive cutting-edge research in biomolecular science, biomedicine, and computational biology. Built upon robust Python-based deep learning and machine learning frameworks, our tools are designed with an emphasis on transparency and reproducibility. Each software package is developed in alignment with our research goals and made publicly available to foster collaboration across the scientific community.

SynProtX

SynProtX is a deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance the prediction of synergistic effects in anti-cancer drug combinations.

GraphEGFR

GraphEGFR is a deep learning model specifically designed to enhance molecular representation for the prediction of inhibitor bioactivity (pIC50) against wild-type HER1, HER2, HER4, and mutant HER1 proteins.

CONTACT

Bundit Boonyarit
Email: [email protected], [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