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A crucial event of protein folding is the formation of a folding core, which is the subset of the protein's structure that is the first to form during folding and the last to break during denaturation. Both experimental and simulation techniques to capture folding core membership have found it challenging. In this paper, the six different computational prediction methods were proposed to predict folding...
A challenging task is to understand the relationship between sequences and folding rates of proteins. Previous studies found that one of contact order (CO), long-range order (LRO), and total contact distance (TCD) has a significant correlation with folding rate of protein. The network concept is increasingly used to describe the topology and dynamics of complex systems. In this paper, the protein...
From the perspective of topology, the native structure of a protein molecule can be represented as a complex network. In the network, amino acids are vertices and the interactions between them act as edges. The networks of 80 proteins that belong to four structural classes are constructed at three length scales: Protein Contact Networks, Long-range Interaction networks and Short-range Interaction...
Identifying nucleus residues is crucial for studying the folding mechanisms of proteins. In this work, the protein structure is modeled as a network with the amino acid residues the vertices and contacts between them the edges. The amino acid networks for native states of 81 proteins are constructed. The amino acid networks have the typical property of small-world network. We performed two independent...
It is a challenging task to investigate the different influence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins are constructed at three length scales: protein contact networks, long-range interaction networks and short-range interaction networks, using complex networks analysis...
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