Iterative Molecular Dynamics—Rosetta Protein Structure Refinement Protocol to Improve Model Quality
نویسندگان
چکیده
منابع مشابه
Iterative Molecular Dynamics—Rosetta Protein Structure Refinement Protocol to Improve Model Quality
Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring function can distinguish native-like from non-native-like conformations in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local energy minimum in which the search algorithm may get stuck. Here, we test the hypothesis that iteration of Rosett...
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Many excellent methods exist that incorporate cryo-electron microscopy (cryoEM) data to constrain computational protein structure prediction and refinement. Previously, it was shown that iteration of two such orthogonal sampling and scoring methods – Rosetta and molecular dynamics (MD) simulations – facilitated exploration of conformational space in principle. Here, we go beyond a proof-of-conc...
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The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffracti...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2013
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct400260c