Investigate the structures and dynamics of biomolecules that are difficult to measure experimentally through simulation.
Life (Saitama University Research Seed Collection 2025-25 p.133)
Keywords: Molecular simulation, biomolecules, integrated modeling, free energy calculation.
Many life phenomena, including various diseases, are caused by biomolecules such as proteins, and observing molecular structures and dynamics in the microscopic realm is crucial for understanding these phenomena and for fundamental treatments of diseases. Molecular dynamics simulation is a technique that allows for the "direct" observation of microscopic behavior by reconstructing biomolecular models with atomic resolution in a computer and moving the molecules according to physical laws. Coupled with the computational power of computers, this technique has developed to the point where it is referred to as a computational microscope and is actively used as a method to complement experiments. However, there are two challenges to contributing to drug discovery and materials development: "too much computation time" and "limitations in model accuracy." To address the first challenge, we are working on introducing efficient algorithms to predict loop structures of next-generation antibodies in a shorter time. For the second challenge, we are developing methods that integrate experimental data and simulations using statistical mathematics and machine learning to achieve more accurate observations.
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Yasuhiro Matsunaga, Associate Professor Graduate School of Science and Engineering, Department of Mathematical and Electronic Information, Information Area 【Recent Research Topics】 ● Prediction of physical properties of next-generation antibodies (VHH) using protein language models ● Analysis of high-speed atomic force microscopy data ● Modeling of viral capsid structures
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【Appeal Points to the Industry】 ● I have experience publishing papers using advanced calculations with supercomputers, multiple commercial software, and full scratch-developed codes in the simulation of biomolecules. ● In drug discovery and materials development, I can support the necessary structural and physical property information derived from simulations to explain experimental results. ● I am available to consult on problems that cannot be solved with commercial molecular modeling software. 【Examples of Practical Applications and Utilization】 ● Development and application of simulation methods for predicting the loop structures of next-generation antibodies (VHH). ● Prediction of denaturation temperatures for next-generation antibodies (VHH). ● Development and application of methods to estimate probe shapes solely from atomic force microscopy image data. ● Elucidation of structures and dynamics through biomolecular simulations utilizing supercomputers.
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The Saitama University Open Innovation Center is a center that functions as a liaison office for industry-academia-government collaboration. It consists of three departments: the Industry-Academia-Government Collaboration Department, the Intellectual Property Department, and the Startup Support Department, each staffed with coordinators well-versed in various fields. The center's activities include solving technical challenges in companies, supporting the implementation of joint research, and conducting technology transfer aimed at introducing and utilizing Saitama University's intellectual property.
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