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Here we use a combined experimental and computational approach to elucidate the early stages of medin nucleation, information that is critical for understanding of the initiation and progression of AMA and protein aggregation in general. The QUARK and ROSETTA methods are broadly comparable in overall methodology, each assembling tertiary structures from structure fragments derived from the PDB, but differ significantly in some aspects such as the fragment libraries, which are fixed in length 3- and 9-residues in ROSETTA but are variable in QUARK and in their scoring functions....