Lattice proteins are highly simplified models of protein-like heteropolymer chains on lattice conformational space which are used to investigate protein folding.[1] Simplification in lattice proteins is twofold: each whole residue (amino acid) is modeled 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.[1] To guarantee the connectivity of the protein chain, adjacent residues on the backbone must be placed on adjacent vertices of the lattice.[2] Steric constraints are expressed by imposing that no more than one residue can be placed on the same lattice vertex.[2]
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,[3] and it is still not possible to fold all real proteins on a computer. Simplification significantly reduces the computational effort in handling the model, although even in this simplified scenario the protein folding problem is NP-complete.[4]
^ abLau KF, Dill KA (1989). "A lattice statistical mechanics model of the conformational and sequence spaces of proteins". Macromolecules. 22 (10): 3986–97. Bibcode:1989MaMol..22.3986L. doi:10.1021/ma00200a030.
^ abCite error: The named reference :1 was invoked but never defined (see the help page).
^Voelz VA, Bowman GR, Beauchamp K, Pande VS (February 2010). "Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)". Journal of the American Chemical Society. 132 (5): 1526–8. doi:10.1021/ja9090353. PMC 2835335. PMID 20070076.
^Berger B, Leighton T (1998). "Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete". Journal of Computational Biology. 5 (1): 27–40. doi:10.1089/cmb.1998.5.27. PMID 9541869.
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