Protein structure prediction based on optimal hydrophobic core formation

The prediction of a minimum energy protein structure from its amino acid sequence represents an important and challenging problem in computational biology. In this paper, we propose a novel heuristic approach for protein structure prediction (PSP) based on the concept of optimal hydrophobic core formation. Using 2D HP model, a well-known set of sub-structures analogous to the secondary structures are obtained. Some sub-conformations are appropriately classified and then incorporated as prior knowledge. Unlike most of the popular PSP approaches which are stochastic in nature, the proposed method is deterministic. The effectiveness of the proposed algorithm is evaluated by well-known benchmark as well as non-benchmark sequences commonly used with 2D HP model. Maintaining similar accuracy as other core based and population based algorithms our method is significantly faster and reduces the computation time as it avoids blind search within the hydrophobic core (H-Core).