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    New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities

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    Publication date
    2016-01-05
    Author
    Towse, Clare-Louise
    Rysavy, S.J.
    Vulovic, I.M.
    Daggett, V.
    Keyword
    Rotamer library; Molecular dynamics simulation; Protein conformation and dynamics; Protein and peptide design
    Peer-Reviewed
    Yes
    
    Metadata
    Show full item record
    Abstract
    Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting and smoothing functions. We resolve these limitations by using physics-based molecular dynamics simulations to determine more accurate frequencies of rotameric states. This work forms part of our Dynameomics initiative and uses a set of 807 proteins selected to represent 97% of known autonomous protein folds, thereby eliminating the bias toward common topologies found within the PDB. Our Dynameomics derived rotamer libraries encompass 4.8 × 10(9) rotamers, sampled from at least 51,000 occurrences of each of 93,642 residues. Here, we provide a backbone-dependent rotamer library, based on secondary structure ϕ/ψ regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication.
    URI
    http://hdl.handle.net/10454/11546
    Version
    No full-text in the repository
    Citation
    Towse C, Rysavy S.J., Vulovic IM (2016) New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. Structure. 24(1):187-199.
    Link to publisher’s version
    http://dx.doi.org/10.1016/j.str.2015.10.017
    Type
    Article
    Collections
    Life Sciences Publications

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