Question

Correlation coefficient for number of amino acid and their weight

Answer 1

For a more detailed description of the interaction between residues, this paper proposes an amino acid network model, which contains two types of weight—similar weight and dissimilar weight. The weight of the link is based on a self-consistent statistical contact potential between different types of amino acids. In this model, we can get a more reasonable representation of the distance between residues. Furthermore, with the network parameter, average shortest path length, we can get a more accurate reflection of the molecular size. This amino acid network is a “small-world” network, and the network parameter is sensitive to the conformation change of protein. For some disease-related proteins, the highly central residues of the amino acid network are highly correlated with the hot spots. In the compound with the related drug, these residues either interacted directly with the drug or with the residue which is in contact with the drug.
Go to:
1. Introduction
In living cells, proteins are very important molecules, and they participate in almost all of the cell functions. During these biological activities, the structure of some proteins shows an obviously conformational flexibility. For a correct and fast implementation of the biological functions through the conformation change, there needs a motor coordination for the residues in different parts of the protein. In this process, a fast communication mechanism is vital for the information sharing between residues about these concerted actions. In fact, this information exchange is achieved through the interaction between residues. But when we put all these residues and the interactions between them together, the protein becomes a very complicated system.