Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
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Arpeggio：用于计算和可视化蛋白质结构中原子间相互作用的Web服务器。
DOI：
10.1016/j.jmb.2016.12.004
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发表时间：
2017-02-03
影响因子：
5.6
通讯作者：
Blundell TL
中科院分区：
文献类型：
--
作者：
Jubb HC;Higueruelo AP;Ochoa-Montaño B;Pitt WR;Ascher DB;Blundell TL
蛋白质与其配体（如小分子、其他蛋白质和DNA）之间的相互作用取决于特定的原子间相互作用，这些相互作用可以根据原子类型、距离和角度约束进行分类。这些相互作用的可视化提供了对分子识别事件性质的深入了解，并在指导药物设计和理解突变的结构和功能影响方面具有实际用途。我们提出了Arpeggio，一个Web服务器，用于计算蛋白质和蛋白质，DNA或小分子配体之间的相互作用，包括货车德瓦尔斯，离子，羰基，金属，疏水和卤素键接触，氢键和特定的原子芳环（阳离子-π，供体-π，卤素-π和碳-π）和芳环芳环（π-π）的相互作用，在用户提交的大分子结构。可以下载PyMOL会话文件，从而生成交互的高质量发布图像。Arpeggio是用Python实现的，可以在http://structure.bioc.cam.ac.uk/arpeggio/上作为一个用户友好的Web界面，也可以在https://bitbucket.org/harryjubb/arpeggio上作为一个可下载的软件包。分子相互作用的枚举和可视化可以促进药物开发，并为理解遗传疾病和蛋白质工程中突变的后果提供见解。可靠和全面的方法来评估和可视化蛋白质结构中存在的许多原子类型之间的全方位潜在分子相互作用是非常宝贵的。Arpeggio在提供的蛋白质数据库文件中计算大分子结构中所有原子内和原子间的相互作用，包括货车德瓦尔斯、离子、羰基、金属、疏水和卤素键接触，以及氢键和特定原子-芳环（阳离子-π、供体-π、卤素-π和碳-π）和芳环-芳环（π-π）相互作用。计算可以在蛋白质、DNA或小有机分子的任何组合之内或之间进行。实现了Arpeggio网络服务器（http：//bleoberis.bioc.cam.ac.uk/arpeggioweb/），以提供一个免费可用的、用户友好的网络界面，用于探索蛋白质结构内的分子相互作用，包括通过基于WebGL的相互作用可视化和可下载的交互式PyMOL会话文件。Arpeggio是用Python编写的，只需要开源依赖项，可以在https://bitbucket.org/harryjubb/arpeggio免费下载，用于自定义分析。
Interactions between proteins and their ligands, such as small molecules, other proteins, and DNA, depend on specific interatomic interactions that can be classified on the basis of atom type and distance and angle constraints. Visualisation of these interactions provides insights into the nature of molecular recognition events and has practical uses in guiding drug design and understanding the structural and functional impacts of mutations. We present Arpeggio, a web server for calculating interactions within and between proteins and protein, DNA, or small-molecule ligands, including van der Waals', ionic, carbonyl, metal, hydrophobic, and halogen bond contacts, and hydrogen bonds and specific atom–aromatic ring (cation–π, donor–π, halogen–π, and carbon–π) and aromatic ring–aromatic ring (π–π) interactions, within user-submitted macromolecule structures. PyMOL session files can be downloaded, allowing high-quality publication images of the interactions to be generated. Arpeggio is implemented in Python and available as a user-friendly web interface at http://structure.bioc.cam.ac.uk/arpeggio/ and as a downloadable package at https://bitbucket.org/harryjubb/arpeggio. Enumeration and visualisation of molecular interactions can facilitate drug development and provide insights towards understanding the consequences of mutations in genetic diseases and protein engineering. Reliable and comprehensive methods to evaluate and visualise the full range of potential molecular interactions across many atom types present in protein structures are invaluable. Arpeggio calculates all intra- and interatomic interactions in macromolecular structures, including van der Waals', ionic, carbonyl, metal, hydrophobic, and halogen bond contacts, and hydrogen bonds and specific atom–aromatic ring (cation–π, donor–π, halogen–π, and carbon–π) and aromatic ring–aromatic ring (π–π) interactions, within a provided Protein Data Bank file. Calculations can be within or between any combination of protein, DNA, or small organic molecules. The Arpeggio web server (http://bleoberis.bioc.cam.ac.uk/arpeggioweb/) was implemented to provide a freely available, user-friendly web interface for the exploration of molecular interactions within protein structures, including through WebGL-based visualisation of interactions and downloadable interactive PyMOL session files. Arpeggio is written in Python, requires only Open Source dependencies, and is freely available for download at https://bitbucket.org/harryjubb/arpeggio for use in custom analyses.