Determination of Protein Structure and Protein Folding Pathways with a Physics-based Coarse-grained

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  Earlier, we demonstrated that three-dimensional structure can be computed for various oligopeptides in several conformational states, and for relatively small proteins (up to 46 residues) with an all-atom representation of the polypeptide chain.Subsequently, we developed a physics-based coarse-grained united-residue (UNRES) model of the polypeptide chain and a related force field to compute the structures of even larger proteins.With the success of this approach with UNRES, this force field was incorporated into a molecular dynamics algorithm to extend the time scale of molecular dynamics and simulate important events in protein folding in real time.
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