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Updated: Jun 14, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein
A Angelini1, A Amato, G Bianconi
1Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy.
Abstract:
We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear, or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese restaurant process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.
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