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Tomii Lab (Molecular Function Informatics Division, National Institute of Advanced Industrial Science and Technology)
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The lab reads the shapes and functions of proteins from vast amounts of biological data.
AboutAbout the lab
Finding biological knowledge in data.
The Tomii Lab studies computational biology, which analyzes biological data with computers.
The lab develops analysis methods that discover new biological knowledge from the vast stores of data on the sequences, structures, and functions of proteins and other molecules.
Its main areas are predicting the three-dimensional structures of proteins and analyzing sequence information.
The lab is located within the Artificial Intelligence Research Center at the National Institute of Advanced Industrial Science and Technology, and students mainly conduct their research there.
Key terms
- Three-dimensional structure
- The three-dimensional shape a protein takes when it folds. Its shape determines its function.
- Alignment
- A method of lining up multiple sequences so that corresponding parts match, making it easy to see where they are similar and where they differ.
- Substrate
- A molecule that binds to a protein such as an enzyme and is acted on by it.
ResearchResearch themes
The lab develops analysis methods for discovering new biological knowledge, and applies them, using diverse and vast data on the sequences, structures, and functions of biological macromolecules. Its core areas are computational structural biology and sequence analysis, but it also conducts research in a wide range of fields in collaboration with computational and experimental researchers at universities and research institutions in Japan and abroad.
*Illustrative imagePredicting protein 3D structures
To predict the three-dimensional structures of proteins and protein complexes from amino acid sequences, the lab develops FORTE, a profile comparison method that searches for similar sequences with high sensitivity. It also develops DeepECA, a deep learning method that predicts contacts between amino acids.
*Illustrative imageFast comparison of substrate-binding sites
Aiming at function prediction from three-dimensional structures and applications to drug discovery, the lab developed a fast method for comprehensively comparing the sites where substrates bind, jointly with the Tsuda Lab. The comparison results are published as the database PoSSuM.
*Illustrative imageFundamental technologies for sequence analysis
For alignment, which is the foundation of computational biology, the lab developed the amino acid substitution matrix MIQS. It has also co-developed fundamental technologies such as MAFFT, a method for computing multiple sequence alignments, and works with a lab at Kyoto University on a method for estimating marine microbes from satellite images.
MembersFaculty
- Visiting ProfessorKentaro Tomii
VoicesStudent voices
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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.
- Top image: “1BT6 tetramer” Boghog2 / Public domain (cropped)
- Predicting protein 3D structures: “Protein structure 2K35” Axel Boldt / Public domain (cropped)
- Fast comparison of substrate-binding sites: “1PWU” Boghog / Public domain (cropped)
- Fundamental technologies for sequence analysis: “C16orf13 MSA” Algh0022 (talk) / Public domain (cropped)
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