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Online Journal of Bioinformatics©
Volume 22 (3): 199-208, 2021.
Near-native protein folding structure simulation
IPP - Bulgarian Academy of Science, Acad. G. Bonchev str, Soa, Bulgaria.
Fidanova S., Near-native protein folding structure simulation, Onl J Bioinform., 22 (3): 199-208, 2021. Protein folding is a fundamental problem in computational molecular biology and biochemical physics. Optimization is based on homologous and hydrophobic-polar (HP) protein model. We used structure elements to predict tertiary structure by HP model on a cubic lattice to determine least energy conformation. The main secondary structures are α helix and β sheets with hydrophobic (H) and polar (P) binary chain monomer. To find most non-consecutive H-H contacts we consider only polypeptide chain with hydrophobic monomers so that minimal energy equates to most H-H. Amino acid sequences determines protein folds for a unique 3D structure with >30% similarity of different structure and function. Conversely, proteins with similar functions and structures can have low AA sequence similarity. Even simplified lattice models cannot find correct structure. Author describes 6 models of helices and sheets hydrophobic-polar (HP) lattices for predicting folding in long chain proteins.
Keywords: Protein folding, Hydrophobic, 3D HP model.