Search our Database of Scientific Publications and Authors

I’m looking for a

    Details and Download Full Text PDF:
    VIPERdb2: an enhanced and web API enabled relational database for structural virology.

    Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
    VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
    PDF Download - Full Text Link
    ( Please be advised that this article is hosted on an external website not affiliated with PubFacts.com)
    Source Status
    http://dx.doi.org/10.1093/nar/gkn840DOI ListingPossible
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686430PMCFound

    Similar Publications

    VIPERdb: a relational database for structural virology.
    Nucleic Acids Res 2006 Jan;34(Database issue):D386-9
    Department of Molecular Biology, TPC-6 The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
    VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Read More
    CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.
    J Struct Biol 2015 Apr 16;190(1):47-55. Epub 2015 Feb 16.
    Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
    Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Read More
    A novel method to map and compare protein-protein interactions in spherical viral capsids.
    Proteins 2008 Nov;73(3):644-55
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
    Viral capsids are composed of multiple copies of one or a few chemically distinct capsid proteins and are mostly stabilized by inter subunit protein-protein interactions. There have been efforts to identify and analyze these protein-protein interactions, in terms of their extent and similarity, between the subunit interfaces related by quasi- and icosahedral symmetry. Here, we describe a new method to map quaternary interactions in spherical virus capsids onto polar angle space with respect to the icosahedral symmetry axes using azimuthal orthographic diagrams. Read More
    A general method to quantify quasi-equivalence in icosahedral viruses.
    J Mol Biol 2002 Dec;324(4):723-37
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
    A quantitative, atom-based, method is described for comparing protein subunit interfaces in icosahedral virus capsids with quasi-equivalent surface lattices. An integrated, normalized value (between 0 and 1) based on equivalent residue contacts (Q-score) is computed for every pair of subunit interactions and scores that are significantly above zero readily identify interfaces that are quasi-equivalent to each other. The method was applied to all quasi-equivalent capsid structures (T=3, 4, 7 and 13) in the Protein Data Bank and the Q-scores were interpreted in terms of their structural underpinnings. Read More