The protein structure is a result of non-covalent interactions between its residues in three-dimensional space.
#DISCLOSED PRINCIPAL DEFINITION FULL#
The results of the reduced model based on principal interactions that were very close to the full interaction model suggest that a new strategy is needed to capture the role of remaining interactions (non-principal interactions) to improve the power of knowledge-based potential functions. This work shows that all interaction types are not equally important in discrimination of native structure. Additionally, the principal interactions consisted of 20 % of the full interactions on average, and they are between residues, which are considered important in protein folding. This method was evaluated on 3 KBPs with different contact definitions and thresholds of distance and revealed that their corresponding principal interactions are very similar and have a lot in common. In fact, the principal interactions maintain the discriminative power of the full interaction model.
We call these interactions as principal interactions and show that the results of the model that considers only these interactions are very close to the full interaction model that considers all interactions in protein fold recognition. We employ a procedure based on the principal component analysis (PCA) to extract the significant and key interactions in native protein structures. In this study, we seek the interaction types that preserve as much of the total potential as possible. Although several KBP functions with different methods have been introduced, the key interactions that capture the total potential have not studied yet. Knowledge-based potentials (KBP) are one type of potential functions derived by known experimentally determined protein structures. The total potential of a protein structure is approximated as the summation of all pair-wise interaction potentials.
Evaluation of protein structure is based on trustworthy potential function.
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