Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.
Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.
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DOI：
10.1016/j.jsb.2010.11.002
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发表时间：
2011-03
影响因子：
3
通讯作者：
Wriggers, Willy
中科院分区：
文献类型：
--
作者：
Birmanns, Stefan;Rusu, Mirabela;Wriggers, Willy
关键词：
我们描述了一个名为Sculptor的集成软件系统，该系统将可视化功能与分子建模算法相结合，用于分析多尺度数据集。雕塑家具有广泛的特殊用途的可视化技术，这些技术基于现代GPU编程，能够实时表示复杂的分子组装。图形和建模的集成提供了几个优势。用户界面不仅缓解了纯算法技术通常陡峭的学习曲线，而且还允许对结果进行即时分析和后处理，以及整合来自外部软件的结果。在这里，我们实现了一种交互式的峰值选择策略，使用户能够探索由SUTERS的COLORES工具生成的初步得分情况。组件的交互放置，一次一个，对于低分辨率或形状模糊的地图是有利的，这些地图有时很难通过全自动的颜色峰值选择来解释。为了后续通过交互和自动峰值选择得到的初步模型的改进，我们在Sculptor和Stus中实现了一种新的同时多体对接，该对接使用互相关系数的归一化来软地执行组件之间的形状互补。建议的技术可在Stus2.6版和Sculptor 2.0版中免费获得。
We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colores tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colores. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0.
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