Model proteins energy

Conformational Adjustments The conformations of protein and ligand in the free state may differ from those in the complex. The conformation in the complex may be different from the most stable conformation in solution, and/or a broader range of conformations may be sampled in solution than in the complex. In the former case, the required adjustment raises the energy, in the latter it lowers the entropy in either case this effect favors the dissociated state (although exceptional instances in which the flexibility increases as a result of complex formation seem possible). With current models based on two-body potentials (but not with force fields based on polarizable atoms, currently under development), separate intra-molecular energies of protein and ligand in the complex are, in fact, definable. However, it is impossible to assign separate entropies to the two parts of the complex. 

A Kitao, S Hayward, N Go. Energy landscape of a native protein Jumpmg-among-mimma model. Proteins 33 496-517, 1998. 

The PDLD model described above is quite useful for evaluating electrostatic free energies in proteins. However, with more computer power one can use... 

Cox, G.A. and Johnston, R.L., Analyzing energy landscapes for folding model proteins, /. Chem. Phys., 124,204714,2006. 

Molecular simulations are used most often for modeling proteins and nucleic acids. We mention the methods here only because they are methods for computing a free energy directly. However, they are rather complex calculations, so we will keep our comments brief. Molecular dynamics simulations give information about the variation in structure and energy of a molecule over an interval of time (78,79). In MD, each atom moves according to Newton s equations of motion for classical particles ... 

The combination of the energy distribution and the number of states that are allowed at each position constitute the alphabet. For model proteins, the complex dynamics of the side chains are often condensed into the energy term fij, whose purpose is usually to model protein stability. The simplest alphabet reduces the information contained in... 

Because the landscape of real proteins is unknown, most of the results we describe in Section III rely on assumptions discussed in Section II. The results are presented for a range of different theoretical landscapes—for example, the random energy model and the uncoupled case—with the assumptions that the real protein landscape lies between these bounds and can be described statistically. Determining the most effective combination of parameters, adjusting them according to the landscape fea-... 

In a similar study, protein evolution has been analyzed using the random energy model (Macken and Perelson, 1989). Macken and Perel-son calculate the probability of a random walk taking k steps to a local optimum as... 

Vorobjev YN, Almagro JC, Hermans J (1998) Discrimination between native and intentionally misfolded conformations of proteins ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model, Proteins, 32 399-413... 

A wide variety of energy functions have been used as part of the various GA-based protein structure prediction protocols. These range from the hydrophobic potential in the simple HP lattice model [19] to energy models such as CHARMM, based on full fledged, detailed molecular mechanics [9]. Apparently, the ease by which various energy functions can be incorporated within the framework of GAs as fitness functions encouraged researchers to modify the energy function in very creative ways to include terms that are not used with the traditional methods for protein structure prediction. 

O Toole, E M, Panagiotopoulos, A. Z. Effect of sequence and intermolecular interactions on the number and nature of low-energy states for simple model proteins J. 

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