▁prote ins , ▁by ▁matching ▁the ▁sequence ▁to ▁struct ural ▁families ▁in ▁the ▁Pf am ▁database . ▁ ▁Dom ains ▁with ▁struct ural ▁hom olog s ▁then ▁follow ▁a ▁" template - based ▁model " ▁( i . e ., ▁hom ology ▁model ing ) ▁protocol . ▁ ▁Here , ▁the ▁Baker ▁labor atory ' s ▁in - house ▁alignment ▁program , ▁K * sync , ▁produces ▁a ▁group ▁of ▁sequence ▁hom olog s , ▁and ▁each ▁of ▁these ▁is ▁mode led ▁by ▁the ▁Ros etta ▁de ▁nov o ▁method ▁to ▁produce ▁a ▁de co y ▁( possible ▁structure ). ▁ ▁The ▁final ▁structure ▁prediction ▁is ▁selected ▁by ▁taking ▁the ▁lowest ▁energy ▁model ▁as ▁determined ▁by ▁a ▁low - resol ution ▁Ros etta ▁energy ▁function . ▁ ▁For ▁domains ▁that ▁have ▁no ▁detected ▁struct ural ▁hom olog s , ▁a ▁de ▁nov o ▁protocol ▁is ▁followed ▁in ▁which ▁the ▁lowest ▁energy ▁model ▁from ▁a ▁set ▁of ▁generated ▁de co ys ▁is ▁selected ▁as ▁the ▁final ▁prediction . ▁ ▁These ▁domain ▁predictions ▁are ▁then ▁connected ▁together ▁to ▁investigate ▁inter - domain , ▁t ert i ary - level ▁interactions ▁within ▁the ▁protein . ▁ ▁Finally , ▁side - chain ▁contributions ▁are ▁mode led ▁using ▁a ▁protocol ▁for ▁Monte ▁Carlo ▁conform ational ▁search . ▁ ▁In ▁C AS P 8 , ▁Rob etta ▁was ▁augment ed ▁to ▁use ▁Ros etta ' s ▁high ▁resolution ▁all - atom ▁ref in ement ▁method , ▁the ▁absence ▁of ▁which ▁was ▁c ited ▁as ▁the ▁main ▁cause ▁for ▁Rob