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Publication - Professor Leo Brady

    CCBuilder

    An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

    Citation

    Wood, CW, Bruning, M, Ibarra, AA, Bartlett, GJ, Thomson, AR, Sessions, RB, Brady, RL & Woolfson, DN, 2014, ‘CCBuilder: An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies’. Bioinformatics, vol 30., pp. 3029-3035

    Abstract

    Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding,
    to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented
    by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.



    Results: We present
    CCBuilder, a web-based application that tackles the problem for a
    defined but large class of protein structure,
    the α-helical coiled coils. CCBuilder generates
    coiled-coil backbones, builds side chains onto these frameworks and
    provides
    a range of metrics to measure the quality of the
    models. Its straightforward graphical user interface provides broad
    functionality
    that allows users to build and assess models, in
    which helix geometry, coiled-coil architecture and topology and protein
    sequence
    can be varied rapidly. We demonstrate the utility
    of CCBuilder by assembling models for 653 coiled-coil structures from
    the
    PDB, which cover >96% of the known coiled-coil
    types, and by generating models for rarer and de novo coiled-coil structures.

    Full details in the University publications repository