Beyond rotamers: a generative,probabilistic model of side chains in proteins |
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Authors: | Tim Harder Wouter Boomsma Martin Paluszewski Jes Frellsen Kristoffer E Johansson Thomas Hamelryck |
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Institution: | (1) The Bioinformatics Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark;(2) DTU Elektro, Technical University of Denmark, Lyngby, Denmark;(3) Department of Chemistry, University of Cambridge, Cambridge, UK;(4) Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Copenhagen, Denmark |
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Abstract: | Background Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein
design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space
is through rotamer libraries - discrete collections of side chain conformations derived from experimentally determined protein
structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this
naturally continuous space comes at the cost of losing detailed information that is crucial for certain applications. For
example, rigorously combining rotamers with physical force fields is associated with numerous problems. |
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