Proposed computational procedure for protein and amyloid structure prediction

Determining the biological activity of a protein requires knowledge about its structure—particularly in the context of correcting the activity profile for a protein with a known structure. The classical dogma is that the structure of a protein is fully determined by its amino acids sequence. As shown on the basis of the FOD-M model, we may reformulate it in the following way: “the residue sequence determines the protein's alignment and degree of deviation from a micelle-like conformation.” A perfectly micellar protein (whose sequence carries little information) are soluble, but incapable of interaction with external molecules, including its specific biological targets. The ability to fulfill a specific biological role is therefore encoded in the form of a localized or global structural disorder (by which we mean deviations from the distribution of hydrophobicity observed in a micelle). For many years, the central problem of protein folding studies has been to devise a model which would enable us to predict the correct biologically active conformation of a protein based on its sequence. The Critical Assessment of Structure Prediction (CASP) challenge has, since 1996, served as a platform for showcasing progress in the area of in silico protein folding models (Liu et al., 2025 and Chen et al., 2024). Recent advances enabled by incorporation of AI methods have resulted in tools such as AlphaFold, with a proven record of accurate structural predictions (Abramson et al., 2024).