Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores

Lattice protein models are used for hierarchical approaches to protein structure prediction, as well as for investigating principles of protein folding. So far, one has the problem that there exists no lattice that can model real protein conformations with good quality and for which an efficient method to find native conformations is known.We present the first method for the FCC-HP-Model [3] that is capable of finding native conformations for real-sized HP-sequences. It has been shown [23] that the FCC lattice can model real protein conformations with coordinate root mean square deviation below 2 Å.Our method uses a constraint-based approach. It works by first calculating maximally compact sets of points (hydrophobic cores), and then threading the given HP-sequence to the hydrophobic cores such that the core is occupied by H-monomers.