MODELLER currently implements a Beale restart conjugate gradients algorithm [#!ShaPhu80!#,#!ACM500!#] and a molecular dynamics procedure with the Verlet integrator [#!Ver67!#]. The conjugate gradients optimizer is usually used in combination with the variable target function method [#!BraGo85!#] which is implemented with the TOP script (Section 3.1). The molecular dynamics procedure can be used in a simulated annealing protocol that is also implemented with the TOP script.