Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. Issue 3 (3rd February 2017)

• Record Type: Journal Article
• Authors: Jubb, Harry C; Higueruelo, Alicia P; Ochoa-Montaño, Bernardo; Pitt, Will R; Ascher, David B; Blundell, Tom L
• Is Part Of: Journal of molecular biology. Volume 429:Issue 3(2017)
• Page Start: 365
• Page End: 371
• Publication Date: 2017-02-03
• Subjects: PDB Protein Data Bank -- SIFt structural interaction fingerprint; protein interactions -- protein–protein interactions -- protein–ligand interactions -- molecular recognition -- drug design; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2016.12.004
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: 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 athttp://structure.bioc.cam.ac.uk/arpeggio/ and as a downloadable package athttps://bitbucket.org/harryjubb/arpeggio . Graphical Abstract: Highlights: 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 athttps://bitbucket.org/harryjubb/arpeggio for use in custom analyses.