FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
复制标题
FRETBursts：用于分析自由扩散单分子 FRET 的开源工具包
作者：
Antonino Ingargiola;E. Lerner;SangYoon Chung;S. Weiss;X. Michalet
单分子Förster共振能量转移（smFRET）允许探测生物大分子中的分子间相互作用和构象变化，是在分子尺度上研究细胞过程的宝贵工具。smFRET实验可以检测3-10 nm范围内的两个荧光标记（供体和受体）之间的距离。在通常采用的共焦几何结构中，分子在溶液中自由扩散。当分子穿过激发体积时，它发射光子的爆发，这可以由单光子雪崩二极管（SPAD）检测器检测到。然后，供体和受体荧光的强度可以与两个荧光团之间的距离相关。虽然近年来已经看到了越来越多的贡献，提出改进或新技术的smFRET数据分析，很少有这些出版物伴随着so.ware的实施。特别是，尽管smFRET的广泛应用，没有完整的软件包的smFRET突发分析是免费的日期。在本文中，我们介绍了FRETBursts，一个开源软件，用于分析自由扩散的smFRET数据。FRET Bursts允许使用最先进的技术和新技术执行smFRET突发分析的所有基本步骤，同时提供开放，强大和有据可查的实施。因此，FRETBursts是比较和开发爆破分析新方法的理想平台。我们采用现代软件工程原理，以尽量减少错误并促进长期可维护性。此外，我们非常注重可重复性，依靠FretBursts执行的笔记本电脑。笔记本是捕获分析所有步骤（包括数据文件、输入参数和结果）的可执行文档，可以轻松共享以复制完整的smFRET分析。笔记本允许初学者执行复杂的工作流程，高级用户可以根据自己的需求自定义分析。通过将分析描述、代码和结果捆绑在一个文档中，FRETBursts允许无缝共享分析工作流程和结果，鼓励重复性并促进单分子社区研究人员之间的合作。
Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3–10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by so.ware implementation. In particular, despite the widespread application of smFRET, no complete so.ware package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and welldocumented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
登录
查看更多内容
用于单分子爆发测量的表观 FRET 效率和荧光光子的平均联合分布的经典最大熵恢复。
DOI：
10.1021/jp209861u
发表时间：
2012
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
DeVore,MatthewS;Gull,StephenF;Johnson,CareyK
通讯作者：
Johnson,CareyK
影响因子：
6.8
作者：
Haran G
通讯作者：
Haran G
影响因子：
7.4
作者：
Santoso, Yusdi;Kapanidis, Achillefs N.
通讯作者：
Kapanidis, Achillefs N.
影响因子：
3.4
作者：
van de Meent, Jan-Willem;Bronson, Jonathan E.;Gonzalez, Ruben L., Jr.
通讯作者：
Gonzalez, Ruben L., Jr.
DOI：
10.1073/pnas.96.7.3670
发表时间：
1999-03-30
影响因子：
11.1
作者：
Deniz, AA;Dahan, M;Schultz, PG
通讯作者：
Schultz, PG