...P) problems are very important subproblems in computational molecular biology. Basically they can be characterized as optimization problems. For a given backbone chain and some residues with rotamers[=-=Dunbrack and Karplus, 1993-=-], solving SCP is to minimize the total energy of this protein, i.e. to find a possibly best protein conformation. Recently, researchers [Althaus et al., 2000, Eriksson et al., 2001, and Kingsford et ...

...ain and some residues with rotamers[Dunbrack and Karplus, 1993], solving SCP is to minimize the total energy of this protein, i.e. to find a possibly best protein conformation. Recently, researchers [=-=Althaus et al., 2000-=-, Eriksson et al., 2001, and Kingsford et al., 2005] use integer linear programming (ILP) method to formulate the SCP, although theoretically it is NP-hard [Pierce and Winfree, 2002]. At almost the sa...

...with rotamers[Dunbrack and Karplus, 1993], solving SCP is to minimize the total energy of this protein, i.e. to find a possibly best protein conformation. Recently, researchers [Althaus et al., 2000, =-=Eriksson et al., 2001-=-, and Kingsford et al., 2005] use integer linear programming (ILP) method to formulate the SCP, although theoretically it is NP-hard [Pierce and Winfree, 2002]. At almost the same time, an equivalent ...