NanoShaper-VMD 接口：计算和可视化分子系统中的表面、口袋和通道。
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.
机构信息
CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy.
BiKi Technologies s.r.l., Genova, Italy.
出版信息
Bioinformatics. 2019 Apr 1;35(7):1241-1243. doi: 10.1093/bioinformatics/bty761.
SUMMARY
NanoShaper is a program specifically aiming the construction and analysis of the molecular surface of nanoscopic systems. It uses ray-casting for parallelism and it performs analytical computations whenever possible to maximize robustness and accuracy of the approach. Among the other features, NanoShaper provides volume, surface area, including that of internal cavities, for any considered molecular system. It identifies pockets via a very intuitive definition based on the concept of probe radius, intrinsic to the definition of the solvent excluded surface. We show here that, with a suitable choice of the parameters, the same approach can also permit the visualisation of molecular channels. NanoShaper has now been interfaced with the widely used molecular visualization software VMD, further enriching its already well furnished toolset.
AVAILABILITY AND IMPLEMENTATION
VMD is available at http://www.ks.uiuc.edu/Research/vmd/. NanoShaper, its documentation, tutorials and supporting programs are available at http://concept.iit.it/downloads.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
NanoShaper 是一个专门针对纳米系统分子表面构建和分析的程序。它使用光线投射实现并行化，并尽可能进行分析计算，以最大限度地提高方法的稳健性和准确性。除其他功能外，NanoShaper 还为任何考虑的分子系统提供体积和表面积，包括内部腔的表面积。它通过基于探针半径概念的非常直观的定义来识别口袋，探针半径是溶剂排除表面定义的固有概念。我们在这里表明，通过选择合适的参数，相同的方法还可以允许可视化分子通道。NanoShaper 现在已经与广泛使用的分子可视化软件 VMD 进行了接口，进一步丰富了其已经非常完善的工具集。
可用性和实现
VMD 可在 http://www.ks.uiuc.edu/Research/vmd/ 获得。NanoShaper、其文档、教程和支持程序可在 http://concept.iit.it/downloads 获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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