A modified amino acid network model contains similar and dissimilar weight.
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.
Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, China. jiaox.china@gmail.com
Xiong
X
Jiao
Lifeng
L
Yang
Meiwen
M
An
Weiyi
W
Chen
D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D015195:Drug Design; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008970:Molecular Weight; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D022021:Tacrolimus Binding Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins; D022021:Tacrolimus Binding Proteins