Journal article
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures
HC Jubb, AP Higueruelo, B Ochoa-Montaño, WR Pitt, DB Ascher, TL Blundell
Journal of Molecular Biology | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Published : 2017
Open access
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 speci..
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Awarded by Medical Research Council
Funding Acknowledgements
First and foremost, we thank Adrian Schreyer; without his pioneering work on CREDO, Arpeggio would not have been possible. We are grateful to Douglas Pires for helpful discussions. H.C.J. was supported by the Biotechnology and Biological Sciences Research Council and UCB [BB/J500574/1]. B.O.-M. was supported by the Bill and Melinda Gates Foundation. D.B.A. is the recipient of a C. J. Martin Research Fellowship from the National Health and Medical Research Council of Australia (APP1072476) and is funded by the Jack Brockhoff Foundation (JBF 4186, 2016) and a Wellcome Trust Programme Grant to TLB (093167/Z/10/Z). D.B.A. and T.L.B. are funded by a Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council and Fundacao de Amparo a Pesquisa do Estado de Minas Gerais (MR/M026302/1). T.L.B. wishes to acknowledge the University of Cambridge and The Wellcome Trust for facilities and support. This work builds on work funded by the Wellcome Trust.