EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Lindert, S., Staritzbichler, R., Wötzel, N., Karakaş, M., Stewart, P., L., & Meiler, J. Structure (London, England : 1993), 17(7):990-1003, 7, 2009. Paper abstract bibtex In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.
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title = {EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.},
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abstract = {In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.},
bibtype = {article},
author = {Lindert, Steffen and Staritzbichler, René and Wötzel, Nils and Karakaş, Mert and Stewart, Phoebe L. and Meiler, Jens},
journal = {Structure (London, England : 1993)},
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