Waseda University
ORCID: 0000-0002-8265-1223Publishes on Protein Structure and Dynamics, Enzyme Structure and Function, Machine Learning in Bioinformatics. 162 papers and 1.3k citations.
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The theory of a one-dimensional lattice gas with long-range many-body interactions is applied to the folding pathways of proteins. This model presents the quantitative informations about the order of inter-residue interactions, the location of nucleation and so on. Three typical proteins are cited as examples and their folding pathways are traced according to the computation of some useful properties.
A one-dimensional lattice gas with long-range many-body interactions is studied by a matrix method for the model of the transition between native and denatured states of globular proteins. The interactions in our model have the nature that two particles situated on two different sites can interact with each other only when all sites between them are occupied by other particles, or in other words, only when they are in a same island which is formed by particles situated side by side. In this system a phase transition occurs in the limit of the infinite long-range interaction and under certain potential functions. The sharpness and the all-or-none type property of the transitions are discussed from the nature of interaction.
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.