Force field parameters protein folding

Energetically, the system is modeled in a similar fashion to its all-atom counterparts. Unlike standard force field calculations, however, simplified versions must capture the bulk effect of solvation and other dominating physical forces through averaged interaction potentials and parameters to fold proteins albeit on a limited basis.[1-3] The energy expression implemented here was first developed by Rey and Skolnick to examine the folding pathways of a-helical hairpin structures. [8] The function applied,... 

Semiempirical functionals intend to reproduce accurate properties using as many semiempirical parameters as needed. The concept of these functionals may be based on the force fields of molecular mechanics, for example, CHARmm (Brooks et al. 1983) and Amber (Pearlman et al. 1995), which have been established to determine the structures of biomacromolecules such as folded proteins. In most cases, the development of such force fields focuses only on constructing potentials to yield highly accurate molecular structures. Likewise, semiempirical functionals have been developed to provide highly accurate properties. Note, however, that... 

CG terms are calibrated on Potential of Mean Forces. These quantities can be extracted either from statistical distributions from the PDB data bank, or from atomistic MD simulations of model systems. Currently, the UNRES force field provides two sets of parameters. The first is calibrated over both structural and folding thermodynamics of G-related albumin-binding module (PDB code IGAB), a triple a-helix bundle. The second set of parameters is calibrated over folding data for tryptophan cage and tryptophan zipper 2 (PDB codes 1L2Y, ILEl), small protein constructs displaying both cx-helical and extended structural elements. 

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