- 著者
- Takeru Kameda Akinori Awazu Yuichi Togashi
- 出版者
- The Biophysical Society of Japan
- 雑誌
- Biophysics and Physicobiology (ISSN:21894779)
- 巻号頁・発行日
- vol.19, pp.e190027, 2022 (Released:2022-09-08)
- 参考文献数
- 211
- 被引用文献数
- 2
With the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure–function relationship is an important topic that highlights the importance of the physicochemical properties of nucleotides, as well as that of amino acids in proteins. Simulations are a useful tool for the detailed analysis of molecular dynamics that complement experiments in molecular biology; however, molecular simulation of nucleic acids is less well developed than that of proteins partly due to the physical nature of nucleic acids. In this review, we briefly describe the current status and future directions of the field as a guide to promote collaboration between experimentalists and computational biologists.
1 0 0 0 OA Screening for mechanical responses of proteins using coarse-grained elastic network models
- 著者
- Yuichi Togashi
- 出版者
- 一般社団法人 電子情報通信学会
- 雑誌
- Nonlinear Theory and Its Applications, IEICE (ISSN:21854106)
- 巻号頁・発行日
- vol.7, no.2, pp.190-201, 2016 (Released:2016-04-01)
- 参考文献数
- 38
- 被引用文献数
- 2
Owing to recent progress in structural biology, the structures of a number of proteins have been resolved and deposited into databases such as the Protein Data Bank (PDB). Many proteins function as molecular machines or show allosteric effects, which require integrated communication between different parts of the protein structure;however, the general principles underlying such communication are not yet clear. All-atom molecular dynamics simulation is a powerful tool for tracking molecular motion, but is still far too computationally costly to be applied widely. In this paper, we present a simple method for assessing the properties of mechanical communications using coarse-grained steered molecular dynamics simulations with elastic network models. The method was tested by screening for a certain mechanical property among protein structures in the PDB.