Lattices models for proteins

DA Elmds, M Levitt. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 243 668-682, 1994. 

D. A. Hinds and M. Levitt, A lattice model for protein structure prediction at low resolution. Proc Natl. Acad. Sci. USA 89, 2536-2540 (1992). 

The complexity of minimalistic lattice models for protein folding... 

Simplified models for proteins are being used to predict their stmcture and the folding process. One is the lattice model where proteins are represented as self-avoiding flexible chains on lattices, and the lattice sites are occupied by the different residues (29). When only hydrophobic interactions are considered and the residues are either hydrophobic or hydrophilic, simulations have shown that, as in proteins, the stmctures with optimum energy are compact and few in number. An additional component, hydrogen bonding, has to be invoked to obtain stmctures similar to the secondary stmctures observed in nature (30). 

Table 3. Predicted Results of Mutations for a Two-Dimensional Square Lattice Model of Protein Folding Using First-Order Sensitivity Theory"...

Force fields must be relatively simple and computationally efficient for studying complex macromolecules such as proteins and DNAs. The force fields usually describe properties of certain types better than others, depending on how the force fields were developed. We have already learned from the sensitivity analysis studies of liquid water and a two-dimensional square lattice model of protein folding that different system properties can be determined by different features of a potential model. 

Shahknovich and Gutin [88] have introduced a 3-D lattice model of protein folding in which amino acids are placed inside a cube in which protein is depicted as a compact self-avoiding chain structure, like one shown in Figure 3.11, which was considered by Sali, Shahknovich, and Karplus [101], As outlined by Sali et al, for such protein models, one can calculate the total energy E of conformation, which is given by the sum of the contact energies between the non-bonded adjacent amino acids within the 3 x 3 x 3 lattice ... 

Sali A, E Shakhnovich and M Karplus 1994b. PCinetics of Protein Folding. A Lattice Model Study of Requirements for Folding to the Native State, journal of Molecular Biology 235 1614-1636. 

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