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Biological Information Engineering Lab
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The lab uses computers to uncover how proteins work.
AboutAbout the lab
Understanding proteins with computers
The Biological Information Engineering Lab uses computers to study how proteins work.
The lab uses a wide range of computational biology methods, including bioinformatics, molecular simulation, and machine learning.
Its work includes calculating how enzymes drive chemical reactions, simulating protein motion, and predicting protein function.
The lab also actively carries out joint research with experimental researchers.
Key terms
- Quantum chemical calculation
- A method that calculates the behavior of electrons based on quantum mechanics to investigate the properties of molecules and how chemical reactions occur
- Molecular dynamics simulation
- A method that calculates the forces acting on atoms and molecules and reproduces their motion over time inside a computer
- Coarse-graining
- A technique that treats several atoms as a single particle, reducing the computational cost so that larger systems and longer timescales can be handled
NewsLab news
A doctoral student won the Poster Award at the 26th Annual Meeting of the Protein Science Society of Japan
A student won the Student Excellent Presentation Award at the 5th Study Group on Biomolecular Simulation and Modeling
A doctoral student won the Student Presentation Award at the 63rd Annual Meeting of the Biophysical Society of Japan
A doctoral student won the Student Excellent Presentation Award at the 38th Molecular Simulation Symposium
ResearchResearch themes
The lab makes full use of computers to clarify the mechanisms by which proteins function. It uses a wide range of computational biology methods, including quantum chemical calculations, molecular dynamics simulations, and machine learning.
*Illustrative imageEnzyme reactions seen through quantum chemical calculations
The lab uses quantum chemical calculations to investigate how enzymes drive chemical reactions. Together with experimental research groups, it analyzes enzymes such as those that produce strigolactone, a plant hormone.
*Illustrative imageProteins seen through simulation
The lab uses molecular dynamics simulations to investigate how proteins work. In collaboration with RIKEN, it studies an iron transporter in plant roots, and it also predicts how strongly drugs block ion channels in the heart.
*Illustrative imageDeveloping coarse-grained simulations
Aiming to handle cell-scale phenomena computationally, the lab develops coarse-graining methods. It builds models that reproduce processes such as proteins assembling into complexes.
*Illustrative imagePredicting protein function with machine learning
The lab develops methods that use machine learning and other techniques to predict protein function by computer. It has also built and publicly released a database of predicted functions for genes involved in biosynthesis.
MembersFaculty
The Biological Information Engineering Lab consists of faculty members, project researchers, joint researchers from agriculture, and doctoral, master's, and undergraduate students.As of 2026
- ProfessorTohru TeradaPublications ↗
- Associate ProfessorHajime SatoPublications ↗
- Project Assistant ProfessorItsuki Negami
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Dynamic simulation screenshot” Jih24 / CC BY-SA 4.0 (cropped)
- Enzyme reactions seen through quantum chemical calculations: “Active site of human ACE2” ChemPro / CC0 (cropped)
- Proteins seen through simulation: “7CN1 viewed from outside” Asai, T.,Adachi, N.,Moriya, T.,Kawasaki, M.,Suzuki, K.,Senda, T.,Murata, T. / CC0 (cropped)
- Developing coarse-grained simulations: “All atom vs coarse grain DPPC bilayer” Christopher Rowley / CC0 (cropped)
- Predicting protein function with machine learning: “TMEM253 AlphaFold Predicted Structure” Liu02511 / CC0 (cropped)
- Related lab (Biochemistry Lab): “House mouse (Mus musculus) 2732” Ahunt / CC0 (cropped)
- Related lab (Bioinformatics Analysis Lab): “Heatmap” Miguel Andrade at English Wikipedia / Public domain (cropped)
- Related lab (Cellular Function Engineering Lab): “Streptomyces hygroscopicus” Snuupo / CC BY-SA 4.0 (cropped)
- Related lab (Plant Functional Engineering Lab): “Arabidopsis thaliana sl13” Stefan.lefnaer / CC BY-SA 4.0 (cropped)
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