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See detailThe early-stage intermediate
Jurkowski, Wiktor UL; Baster, Z.; Dulak, D. et al

in Roterman-Konieczna, I. (Ed.) Protein Fold Silico Protein Fold Versus Protein Struct Predict (2012)

The multistep polypeptide chain folding model presented in this chapter involves several intermediates, the first of which is called the early-stage (ES) intermediate. This intermediate is assumed to be ... [more ▼]

The multistep polypeptide chain folding model presented in this chapter involves several intermediates, the first of which is called the early-stage (ES) intermediate. This intermediate is assumed to be defined solely on the basis of the backbone conformation and does not take side chains into account. The geometric principles that guide the backbone alignment process and its quantitative influence on the structural arrangement of the folded chain can be expressed by means of a contingency table, linking known structural motifs to specific polypeptide sequences. The basic unit of this algorithm is the tetrapeptide, and the corresponding ES conformational subspace is assumed to consist of seven types of motifs. This limited subspace represents a subset of the full conformational space (i.e., the Ramachandran plot). The volumetric structure of the ES intermediate corresponds to the output of the early folding stage and, simultaneously, provides input for further stages of the folding process. [less ▲]

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