RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps
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DOI：
10.1093/bioinformatics/btu841
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发表时间：
2015-05-01
期刊：
影响因子：
5.8
通讯作者：
Ferrin, Thomas E.
中科院分区：
文献类型：
--
作者：
Chen, Jonathan E.;Huang, Conrad C.;Ferrin, Thomas E.
动机：接触图是结构生物学家通过二维简化来识别结构特征的一种方便方法。具有单个截止距离的二元（是/否）接触图可以推广到显示连续的距离范围。我们已经开发了一个UCSF嵌合体工具，RRDistMaps，计算这样的广义地图，以分析分子内接触的成对变化。一个交互式的实用程序，RRDistMaps，可视化的构象变化，无论是本地（如结合位点残基）和全球（如铰链运动），通过距离模式之间的未绑定和绑定的蛋白质。用户可以在RRDistMaps中定位残基对，以便在Chimera中进一步导航。该界面包含识别长距离残留物运动和比对序列的独特功能，可同时比较距离图。
Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns. Users can target residue pairs in RRDistMaps for further navigation in Chimera. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.