Lattice protein

Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.

Because proteins are such large molecules, there are severe computational limits on the simulated timescales of their behaviour when modeled in all-atom detail. The millisecond regime for all-atom simulations was not reached until 2010, and it is still not possible to fold all real proteins on a computer. Simplification in lattice proteins is twofold: each whole residue (amino acid) is modelled as a single "bead" or "point" of a finite set of types (usually only two), and each residue is restricted to be placed on vertices of a (usually cubic) lattice. To guarantee the connectivity of the protein chain, adjacent residues on the backbone must be placed on adjacent vertices of the lattice. Sterical constraints are simply expressed by imposing that no more than one residue could be placed on the same lattice vertex. Simplifications of this kind significantly reduce the computational effort in handling the model, although even in this simplified scenario the protein folding problem is NP-complete.

Different versions of lattice proteins may adopt different types of lattice (typically square and triangular ones), in two or three dimensions, but it has been shown that generic lattices can be used and handled via a uniform approach.

Lattice proteins are made to resemble real proteins by introducing an energy function, a set of conditions which specify the interaction energy between neighbouring beads, usually those occupying adjacent lattice sites. The energy function mimics the interactions between amino acids in real proteins, which include steric, hydrophobic and hydrogen bonding effects. The beads are divided into types, and the energy function specifies the interactions depending on the bead type, just as different types of amino acids interact differently. One of the most popular lattice models, the HP model, features just two bead types—hydrophobic (H) and polar (P)—and mimics the hydrophobic effect by specifying a negative (i.e. favourable) interaction between H beads.

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