TopoStats - A program for automated tracing of biomolecules from AFM images.
TopoStats - A program for automated tracing of biomolecules from AFM images.
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TopoStats -一个从AFM图像自动跟踪生物分子的程序。
DOI：
10.1016/j.ymeth.2021.01.008
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发表时间：
2021-09
期刊：
影响因子：
--
通讯作者：
Pyne ALB
中科院分区：
文献类型：
--
作者：
Beton JG;Moorehead R;Helfmann L;Gray R;Hoogenboom BW;Joseph AP;Topf M;Pyne ALB
TopoStats是一个用于自动化AFM数据处理的Python工具包。TopoStats将原始数据作为输入，并在没有用户输入的情况下输出处理后的数据和统计信息。TopoStats可以精确地追踪线性和环状生物分子，并提供构象分析。我们应用TopoStats分析DNA微环，折纸和孔形成蛋白。TopoStats可用于理想样本和污染样本。TopoStats是一个Python工具包，用于自动编辑和分析原子力显微镜图像。该程序自动识别和跟踪单个分子的环状和线性构象，而无需用户输入。TopoStats能够在AFM图像中识别和追踪一系列分子，在宽视场内平均发现约90%的所有单个分子和分子组装体，而无需事先处理。不同大小的DNA微环、DNA折纸环和孔形成蛋白被鉴定并用通常在预测轮廓长度的10 nm内的迹线的轮廓长度准确地追踪。TopoStats还能够可靠地识别和追踪混合群体中的线性和封闭的环状分子。该程序可通过GitHub（https：//github.com/afm-spm/TopoStats）免费获得，并可根据需要进行修改和调整。
TopoStats is a Python toolkit for automated AFM data processing. TopoStats takes raw data as input, and outputs processed data and statistical information without user input. TopoStats can accurately trace linear and circular biomolecules and provide conformational analysis. We applied TopoStats to analyse DNA minicircles, origami and pore-forming proteins. TopoStats can be used on both ideal and contaminated samples. We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, ~90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub (https://github.com/afm-spm/TopoStats) and is intended to be modified and adapted for use if required.
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影响因子：
16.6
作者：
Irobalieva RN;Fogg JM;Catanese DJ Jr;Sutthibutpong T;Chen M;Barker AK;Ludtke SJ;Harris SA;Schmid MF;Chiu W;Zechiedrich L
通讯作者：
Zechiedrich L
影响因子：
16.6
作者：
Pyne ALB;Noy A;Main KHS;Velasco-Berrelleza V;Piperakis MM;Mitchenall LA;Cugliandolo FM;Beton JG;Stevenson CEM;Hoogenboom BW;Bates AD;Maxwell A;Harris SA
通讯作者：
Harris SA
影响因子：
2.1
作者：
van der Walt, Stefan;Colbert, S. Chris;Varoquaux, Gael
通讯作者：
Varoquaux, Gael
影响因子：
9.4
作者：
Valero-Rello A;Henares D;Acosta L;Jane M;Jordan I;Godoy P;Muñoz-Almagro C
通讯作者：
Muñoz-Almagro C
影响因子：
38.3
作者：
Valero J;Pal N;Dhakal S;Walter NG;Famulok M
通讯作者：
Famulok M