“…There are many such methods, exploiting different protein representations, energy function terms, and optimization or enumeration algorithms. The search algorithms include sampling of main-chain dihedral angles biased by their distributions in known protein structures~Moult & James, 1986!, minimum perturbation random tweak method~Fine Shenkin et al, 1987;Smith & Honig, 1994!, systematic conformational search~Bruccoleri & Karplus, 1987Bruccoleri et al, 1988;Brower et al, 1993;Bruccoleri, 1993!, global energy minimization by mapping a trajectory of local minima~Dudek & Scheraga, 1990;Dudek et al, 1998!, importance sampling by local minimization of randomly generated conformations~Lambert & Scheraga, 1989a, 1989b, 1989c!, local energy minimization~Mattos et al, 1994!, molecular dynamics simulations~Bruccoleri & Karplus, 1990Tanner et al, 1992;Rao & Teeter, 1993;Nakajima et al, 2000!, genetic algorithms~McGarrah & Judson, 1993Ring & Cohen, 1994!, biased probability Monte Carlo search~Abagyan & Totrov, 1994Evans et al, 1995;Thanki et al, 1997!, Monte Carlo with simulated annealing~Higo et al, 1992Carlacci & Englander, 1993Collura et al, 1993;Vasmatzis et al, 1994!, Monte Carlo and molecular dynamics~Rapp & Friesner, 1999!, extended-scaled-collective-variable Monte Carlo~Kidera, 1995!, scaling relaxation and multiple copy sampling~Rosenfeld et al, 1993Zheng et al, 1993aZheng et al, , 1993bRosenbach & Rosenfeld, 1995!, searching through discrete conformations by dynamic programming~Vajda &…”