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Biomolecular Dynamics Modeling Lab
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The lab uses computational modeling to explore how protein structures move.
AboutAbout the lab
Moving between experimental data and computation to explore how molecules move
The Biomolecular Dynamics Modeling Lab develops computational methods for modeling biomolecules and for studying changes in molecular shape (conformational dynamics).
Because experimental and structural data are growing rapidly, the lab believes that even more sophisticated methods are needed to understand how biomolecules work in a more realistic way.
The lab combines bioinformatics and data analysis methods to carry out modeling and simulation using existing data.
On the lab's website, it is introduced under the English name 'Laboratory for Biomolecular Modeling and Design (LBMAD).'
Key terms
- Conformation
- The three-dimensional shape that a molecule such as a protein adopts. Even the same molecule can change its shape.
- Bioinformatics
- A field that organizes and analyzes data obtained from living organisms using methods from information science.
- Allostery
- The phenomenon in which a change at one site in a protein affects the function of a distant site.
ResearchResearch themes
To understand how biomolecules work in a more realistic way, the lab develops computational methods for building molecular models and investigating their motion. It carries out modeling and simulation using existing data, and also uses these methods to analyze and interpret experimental data.
*Illustrative imageMoving Back and Forth Between Experimental Data and Computational Modeling
The lab carries out modeling and simulation using the growing volume of experimental and structural data, and uses these methods to analyze and interpret experimental data. As data increases, more analysis workflows and methods are needed as well.
*Illustrative imageAllostery and Protein-Protein Interactions
The lab studies allostery, oligomerization, interactions between proteins, and the conservation of structure and dynamics. Its targets include TIM-barrel proteins, PyrR, dihydrofolate reductase, and leukotriene A4 hydrolase.
MembersFaculty
- Independent Associate ProfessorSandhya P. Tiwari
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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: “TriosePhosphateIsomerase Ribbon pastel” Dcrjsr / CC BY 3.0 (cropped)
- Moving Back and Forth Between Experimental Data and Computational Modeling: “Molecular Modeling” derivative work: Dhatfield (talk) MM_PEF.svg: Edboas / CC BY-SA 3.0 (cropped)
- Allostery and Protein-Protein Interactions: “STRING 12.0 SBK3 Protein Interactions” STRING CONSORTIUM 2023 / CC BY 4.0 (cropped)
- Related lab (計算生物学研究室
（水口研） ): “Linuron-3D-molecular-model-engraved-render-CAS-330-55-2” MolGod Scientific / CC BY-SA 4.0 (cropped) - Related lab (蛋白質構造データバンク構築研究室): “Neuraminidase Ribbon Diagram” NASA / Public domain (cropped)
- Related lab (細胞システム研究室
（岡田研） ): “Fluorescence micrograph of Thalassiosira nanae” Terry J. McGenity, Amare Gessesse, John E. Hallsworth, Esther Garcia Cela, Carol Verheecke-Vaessen, Fengping Wang, Max Chavarría, Max M. Haggblom, Søren Molin, Antoine Danchin, Eddy J. Smid, Cédric Lood, Charles S. Cockell, Corinne Whitby, Shuang-Jiang Liu, Nancy P. Keller, Lisa Y. Stein, Seth R. Bordenstein, Rup Lal, Olga C. Nunes, Lone Gram, Brajesh K. Singh, Nicole S. Webster, Cindy Morris, Sharon Sivinski, Saskia Bindschedler, Pilar Junier, André Antunes, Bonnie K. Baxter, Paola Scavone and Kenneth Timmis Photograph by Philippe Laissue. / CC BY-SA 4.0 (cropped) - Related lab (細胞機能
デザイン研究室 （戸田研） ): “Synthetic Biology Research at NASA Ames” Alexander van Dijk from San Francisco, United States / CC BY 2.0 (cropped)
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