RECOGNITION OF PROTEIN-STRUCTURE ON COARSE LATTICES WITH RESIDUE-RESIDUE ENERGY FUNCTIONS

We suggest and test potentials for the modeling of protein structure o n coarse lattices, The coarser the lattice, the more complete and fast er is the exploration of the conformational space of a molecule, Howev er, there are inevitable energy errors in lattice modeling caused by d istortions in distances between interacting residues; the coarser the lattice, the larger are the energy errors, It is generally believed th at an improvement in the accuracy of lattice modelling can be achieved only by reducing the lattice spacing, We reduce the errors on coarse lattices with lattice-adapted potentials, Two methods are used: in the first approach, 'lattice-derived' potentials are obtained directly fr om a database of lattice models of protein structure; in the second ap proach, we derive 'lattice-adjusted' potentials using our previously d eveloped method of statistical adjustment of the 'off-lattice' energy functions for lattices, The derivation of off-lattice C-alpha atom-bas ed distance-dependent pair,vise potentials has been reported previousl y, The accuracy of 'lattice-derived', 'lattice-adjusted' and 'off-latt ice' potentials is estimated in threading tests, It is shown that 'lat tice-derived' and 'lattice-adjusted' potentials give virtually the sam e accuracy and ensure reasonable protein fold. recognition on the coar sest considered lattice (spacing 3.8 Angstrom), however, the 'off-latt ice' potentials, which efficiently recognize off-lattice folds, do not work on this lattice, mainly because of the errors in short-range int eractions between neighboring residues.