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Protein Design Lab
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A lab that designs proteins from scratch on computers.
AboutAbout the lab
Designing proteins from scratch on computers.
The Protein Design Lab designs proteins on computers based on physical chemistry and data science, and studies how their structures form and the principles by which their functions emerge.
The lab believes that natural proteins are finished products that nature has spent billions of years creating, and that analyzing them alone makes it difficult to clarify the mechanisms by which they work.
The lab uses biochemical experiments to examine how the designed proteins actually behave, and uses the results to develop protein design technology.
The lab is located in the Advanced Protein Data Science Research Center (ASPiRE), part of the Institute for Protein Research at Osaka University, and the site also introduces it under the name "Koga Lab."
Key terms
- Amino acid sequence
- The order in which the amino acids that make up a protein are arranged. A protein folds into a defined three-dimensional structure according to this order.
- Backbone structure
- The shape of the part that forms the skeleton of the chain of linked amino acids. It is described by features such as secondary structure and loop length.
- Molecular simulation
- A method of studying the movements and behavior of molecules by reproducing them on a computer.
NewsLab news
View More ↗ResearchResearch themes
Proteins fold into defined three-dimensional structures according to their amino acid sequences and carry out their functions. The lab designs proteins on computers from hypotheses based on physical chemistry and data science, and examines their behavior through biochemical experiments. It aims to clarify the principles by which structures form and functions emerge, and to develop protein design technology.
*Illustrative imageDesigning novel proteins from scratch
Using analysis of natural protein data, molecular simulation, and biochemical experiments, the lab develops methods to design proteins completely from scratch. Focusing on backbone structure, such as secondary structure and loop length, it has designed proteins of various shapes with atomic-level accuracy.
*Illustrative imageRemodeling natural proteins
Using the technology developed through de novo design, the lab substantially remodels natural proteins, taking on the challenge of improving their stability and giving them new functions. It has succeeded in making a polyethylene terephthalate (PET)-degrading enzyme more heat-resistant and in adding a new allosteric site to V1-ATPase, a rotary molecular motor.
MembersFaculty
The members of the Protein Design Lab are faculty, researchers, master's students, and non-degree research students.As of 2026
- ProfessorNobuyasu Koga
- Assistant ProfessorRie Koga
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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: “TMEM238 protein predicted folding via AlphaFold” Huntingrl / CC0 (cropped)
- Designing novel proteins from scratch: “Homemade Protein Structural Model” Bennettscience / CC BY 2.0 (cropped)
- Remodeling natural proteins: “Protein Crystal Malic Enzyme” NASA / Public domain (cropped)
- Related lab (Biological Regulation Lab): “Fluorescence.microscope1” Bioguy10 / CC0 (cropped)
- Related lab (Biomolecular Recognition Lab): “Human tyrosyl-tRNA synthetase (interdomain interaction, TyrRS)” Oleksandr V. Savytskyi / CC BY 4.0 (cropped)
- Related lab (Molecular Developmental Biology Lab): “Confocal Microscope” Mark from Edinburgh, United Kingdom / CC BY-SA 2.0 (cropped)
- Related lab (Interdisciplinary Group (Nuclear Function) Lab): “Yeast cells in wet mount of culture” Ajay Kumar Chaurasiya / CC BY-SA 4.0 (cropped)
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