Classification of protein quaternary structure by functional domain composition

To explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11%Compared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.The structure hierarchy of proteins is defined in terms of four levels: primary, secondary, tertiary, and quaternary. The term quaternary structure was first introduced by Bernal in 1958 [1-3]. It refers to the non-covalent interactions of protein subunits to form oligomers and the spatial arrangement of the subunits.Oligomeric proteins are very common in nature. They can be divided further into two classes: homo-oligomers and hetero-oligomers; the former are composed of identical subunits while the latter are composed of non-identical subunits. For example, the potassium channel is formed by a homo-tetramer [4] , and the gamma-aminobytyric acid type A (GABAA) receptor is formed by a hetero-pentamer [5]. The subunit construction of proteins provides the structural basis for their activities and functions in various biological processes, which include metabolism, signal transduction and chromosome replication [3,6]. From an evolutional point of view, the oligomeric proteins have more advantages than the monomers [7,8]. It is easier for multi-subunit proteins to repair their defects by s