BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
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BioAfmViewer：用于模拟生物分子结构和动力学的AFM扫描的交互式界面。
DOI：
10.1371/journal.pcbi.1008444
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发表时间：
2020-11
影响因子：
4.3
通讯作者：
Flechsig H
中科院分区：
文献类型：
--
作者：
Amyot R;Flechsig H
我们提供了一个独立的软件，BioAFMviewer，它将生物分子结构转换成对应于原子力显微镜（AFM）实验结果的图形表示。AFM图形是通过对相应PDB文件中编码的分子结构进行模拟扫描而获得的。一个多功能的分子观察器集成了PDB结构的可视化和对它们的方向的控制，而同步模拟扫描与可变的空间分辨率和尖端形状的几何形状产生相应的AFM图形。我们证明了BioAFMviewer的适用性，通过比较模拟AFM图形高速AFM观察蛋白质。该软件还可以处理构象运动的分子电影，例如从对蛋白质内的功能转变进行建模的服务器获得的那些，并产生相应的模拟AFM电影。BioAFMviewer软件提供了一个平台，可以利用蛋白质的大量结构和动力学数据来帮助解释生物分子AFM实验。如今，纳米技术允许观察工作中的单个蛋白质。在原子力显微镜（AFM）下，例如，其表面可被快速扫描并监测功能运动，这对于生命科学的各个领域的应用具有重要意义。然而，实验结果的分析和解释仍然具有挑战性，因为获得的图像或分子电影的分辨率远非完美。另一方面，大多数蛋白质的高分辨率静态结构是已知的，它们的构象动力学可以在分子模拟中计算。这一巨大的可用数据量为更好地了解分辨率受限扫描实验的结果提供了很好的机会。我们的软件提供了实现这一目标的计算包。BioAFMviewer通过计算模拟任何生物分子结构的扫描，以产生模拟AFM实验结果的图形图像。这使得所有可用的结构数据和计算分子电影与AFM结果的比较成为可能。我们表明，模拟AFM图像是非常有价值的，以方便高速AFM观测的解释。凭借其多功能的交互界面和丰富的功能，BioAFMviewer为广泛的Bio-AFM社区提供了一个方便的平台，以更好地了解实验。
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments. Nowadays nanotechnology allows to observe single proteins at work. Under atomic force microscopy (AFM), e.g., their surface can be rapidly scanned and functional motions monitored, which is of great importance for applications in all fields of Life science. The analysis and interpretation of experimental results remains however challenging, because the resolution of obtained images or molecular movies is far from perfect. On the other side, high-resolution static structures of most proteins are known and their conformational dynamics can be computed in molecular simulations. This enormous amount of available data offers a great opportunity to better understand the outcome of resolution-limited scanning experiments. Our software provides the computational package towards this goal. The BioAFMviewer computationally emulates the scanning of any biomolecular structure to produce graphical images that mimic the outcome of AFM experiments. This makes the comparison of all available structural data and computational molecular movies to AFM results possible. We demonstrate that simulated AFM images are of great value to facilitate the interpretation of high-speed AFM observations. With its versatile interactive interface and rich functionality, the BioAFMviewer provides a convenient platform for the broad Bio-AFM community to better understand experiments.
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影响因子：
16.6
作者：
Shibata M;Nishimasu H;Kodera N;Hirano S;Ando T;Uchihashi T;Nureki O
通讯作者：
Nureki O
影响因子：
14.9
作者：
wwPDB consortium
通讯作者：
wwPDB consortium
影响因子：
6.8
作者：
Heath, George R.;Scheuring, Simon
通讯作者：
Scheuring, Simon
影响因子：
14.9
作者：
Suhre, K;Sanejouand, YH
通讯作者：
Sanejouand, YH
DOI：
10.1098/rstb.2017.0180
发表时间：
2018-06-19
影响因子：
6.3
作者：
Noshiro, Daisuke;Ando, Toshio
通讯作者：
Ando, Toshio