Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 429, Issue 3, Pages 365-371Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2016.12.004
Keywords
protein interactions; protein protein interactions; protein ligand interactions; molecular recognition; drug design
Categories
Funding
- Biotechnology and Biological Sciences Research Council
- UCB [BB/J500574/1]
- Bill and Melinda Gates Foundation
- C. J. Martin Research Fellowship from the National Health and Medical Research Council of Australia [APP1072476]
- Jack Brockhoff Foundation [JBF 4186]
- Wellcome Trust [093167/Z/10/Z]
- Newton Fund RCUK-CONFAP by The Medical Research Council
- Fundacao de Amparo a Pesquisa do Estado de Minas Gerais [MR/M026302/1]
- University of Cambridge
- Wellcome Trust
- Biotechnology and Biological Sciences Research Council [1103577] Funding Source: researchfish
- Medical Research Council [MR/M026302/1] Funding Source: researchfish
- MRC [MR/M026302/1] Funding Source: UKRI
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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-pi, donor-pi, halogen-pi, and carbon-pi) and aromatic ring aromatic ring (pi-pi) 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. Crown Copyright (C) 2016 Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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