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Updated: Sep 15, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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OpenCafeMol:在GPU上的一种粗粒度的生物分子模拟器,用于囊泡融合

Yutaka Murata1, Toru Niina2, Shoji Takada1

  • 1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.

Biophysical journal
|July 14, 2025
PubMed
概括

OpenCafeMol是一款新的分子动力学 (MD) 软件,可以在GPU上加速生物分子模拟. 这种快速,灵活的工具可以对蛋白质和脂质膜进行更长的模拟,有助于膜融合研究.

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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The fluid mosaic model was first proposed as a visual representation of research observations. The model comprises the composition and dynamics of membranes and serves as a foundation for future membrane-related studies. The model depicts the structure of the plasma membrane with a variety of components, which include phospholipids, proteins, and carbohydrates. These integral molecules are loosely bound, defining the cell’s border and providing fluidity for optimal function.
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α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
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