cellPACK：用于建模和可视化结构系统生物学的虚拟介观模拟器。
cellPACK: a virtual mesoscope to model and visualize structural systems biology.
机构信息
1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA. [3] California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
出版信息
Nat Methods. 2015 Jan;12(1):85-91. doi: 10.1038/nmeth.3204. Epub 2014 Dec 1.
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.
cellPACK 可组装生物中尺度（介于分子和细胞生物学尺度之间的 10-100nm 范围）的计算模型。cellPACK 的模块化架构集成了现有和新颖的填充算法，用于生成、可视化和分析整合来自多个实验系统生物学和结构生物学源数据的复杂生物环境的综合三维模型。cellPACK 作为开源代码提供，具有模型验证工具以及五个生物学系统的“食谱”和模型：血浆、细胞质、突触小泡、HIV 和支原体细胞。我们已经应用 cellPACK 对 HIV 包膜蛋白的分布进行建模，以根据实验观察对几种假设进行一致性测试。生物学家、教育工作者和外展专家可以通过 http://cellPACK.org/ 中的脚本和图形用户界面与 cellPACK 模型进行交互、开发新的食谱和执行填充实验。
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