Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

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• 作者：Harry C Jubb¹ ; ^§ ; ; ^{hj4@sanger.ac.uk} ; ^{harry.jubb@gmail.com} ; ^{hj251@cam.ac.uk} ; Alicia P Higueruelo¹ ; Bernardo Ochoa-Montañ ; o¹ ; Will R Pitt² ; David B Ascher¹ ; ^{david.ascher@unimelb.edu.au} ; Tom L Blundell¹ ; ^{tlb20@cam.ac.uk}
• 关键词：PDB ; Protein Data Bank ; SIFt ; structural interaction fingerprint
• 刊名：Journal of Molecular Biology
• 出版年：2017
• 出版时间：3 February 2017
• 年：2017
• 卷：429
• 期：3
• 页码：365-371
• 全文大小：1257 K
• 卷排序：429

文摘

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.