An on/off lattice approach to protein structure prediction from contact maps

An important unsolved problem in structural bioinformatics is that of protein structure prediction (PSP), the reconstruction of a biologically plausible three-dimensional structure for a given protein given only its amino acid sequence. The PSP problem is of enormous interest, because the function of proteins is a direct consequence of their three-dimensional structure. Approaches to solve the PSP use protein models that range from very realistic (all-atom) to very simple (on a lattice). Finer representations usually generate better candidate structures, but are computationally more costly than the simpler on-lattice ones. In this work we propose a combined approach that makes use of a simple and fast lattice protein structure prediction algorithm, REMC-HPPFP, to compute a number of coarse candidate structures. These are later refined by 3Distill, an off-lattice, residue-level protein structure predictor. We prove that the lattice algorithm is able to bootstrap 3Distill, which conseque...