Grigoriev I V, Rakhmaninova A B, Mironov A A
Research Institute for Genetics of Industrial Microorganisms, Moscow, Russia.
J Biomol Struct Dyn. 1998 Aug;16(1):115-22. doi: 10.1080/07391102.1998.10508232.
A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on a vicinity of "molten globule" states of a protein. In contrast to the majority of the known approaches for estimation of a protein free energy we introduce a simplified potential of interactions with solvent and consider conformational energy of the loops in addition to mean-force potential. The model was applied to several globular alpha-helical proteins and demonstrated high prediction accuracy in comparison with other known models.
