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J Mol Biol. 2017 Feb 3;429(3):365-371. doi: 10.1016/j.jmb.2016.12.004. Epub 2016 Dec 10.

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

Author information

1
Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: hj4@sanger.ac.uk.
2
Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
3
UCB, 208 Bath Road, Slough, West Berkshire SL1 3WE, UK.
4
Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: david.ascher@unimelb.edu.au.
5
Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: tlb20@cam.ac.uk.

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 at http://structure.bioc.cam.ac.uk/arpeggio/ and as a downloadable package at https://bitbucket.org/harryjubb/arpeggio.

KEYWORDS:

drug design; molecular recognition; protein interactions; protein–ligand interactions; protein–protein interactions

PMID:
27964945
PMCID:
PMC5282402
DOI:
10.1016/j.jmb.2016.12.004
[Indexed for MEDLINE]
Free PMC Article

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