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

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          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.

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          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 at https://bitbucket.org/harryjubb/arpeggio for use in custom analyses.

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          Most cited references32

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          PLIP: fully automated protein–ligand interaction profiler

          The characterization of interactions in protein–ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein–ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein–ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web . The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein–ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling.
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            The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

            The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.
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              Satisfying hydrogen bonding potential in proteins.

              We have analysed the frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules. There are a small percentage of nitrogen or oxygen atoms that do not form hydrogen bonds with either solvent or protein atoms, when standard criteria are used. For high resolution structures 9.5% and 5.1% of buried main-chain nitrogen and oxygen atoms, respectively, fail to hydrogen bond under our standard criteria, representing 5.8% and 2.1% of all main-chain nitrogen and oxygen atoms. We find that as the resolution of the data improves, the percentages fall. If the hydrogen bond criteria are relaxed many of these unsatisfied atoms form weak hydrogen bonds. However, there remain some buried atoms (1.3% NH and 1.8% CO) that fail to hydrogen bond without any immediately obvious compensating interactions.
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                Author and article information

                Contributors
                Journal
                J Mol Biol
                J. Mol. Biol
                Journal of Molecular Biology
                Elsevier
                0022-2836
                1089-8638
                03 February 2017
                03 February 2017
                : 429
                : 3
                : 365-371
                Affiliations
                [1 ]Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
                [2 ]UCB, 208 Bath Road, Slough, West Berkshire SL1 3WE, UK
                Author notes
                [§]

                Present Addresses: H.C. Jubb, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; A.P. Higueruelo, Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK; D.B. Ascher, Department of Biochemistry, Bio21, University of Melbourne, Victoria, Australia.

                Article
                S0022-2836(16)30533-2
                10.1016/j.jmb.2016.12.004
                5282402
                27964945
                31fe1fd1-1174-4f9d-b54f-f1546a218300
                Crown Copyright © 2016 Published by Elsevier Ltd. All rights reserved.

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 5 July 2016
                : 7 November 2016
                : 6 December 2016
                Categories
                Databases/Web Servers

                Molecular biology
                pdb, protein data bank,sift, structural interaction fingerprint,protein interactions,protein–protein interactions,protein–ligand interactions,molecular recognition,drug design

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