For the first half of the residency program, simulated procedures were not recorded separately from actual procedures performed on patients.
The simulated annealing procedure was carried out in vacuo (dielectric constant = 1) considering that in MODELLER, the effect of solvation, like electrostatics, is assumed to be encoded in the template structure and thus in the distance restraints derived from the template.
Firstly, a simulated annealing procedure was used to generate low potential energy structures of I.
The simulated annealing procedure was repeated with different initial velocities to generate an ensemble of 200 structures.
When AMOVA analysis could not determine what number of partitioned groups is the most suitable, a spatial analysis of molecular variance (SAMOVA) based on a simulated annealing procedure was used to define the groups of populations [ 33].
The injury model, as well as any other simulated surgical procedure, is assumed to be performed by surgeons or qualified scientists using standard techniques.
Strategies for setting reasonable penalty factor in objective function and temperature in simulated annealing procedure were proposed.
The heuristic begins on a well-designed initial solution generator; then a simulated annealing procedure is applied for further improvement of the solution.
The temperatures used in the simulated annealing procedure were 150 K, 250 K, 400 K, 1000 K for heating and 800 K, 600 K, 500 K, 400 K, 300 K for cooling.
(A basic description of the methods incorporated in AMBER is given elsewhere [21].) The starting models for the simulated annealing procedure are either crystal structures of phosphopeptide-SH2 domain complexes, or – where such structures are not available – models built by mutating phosphopeptide residues from a closely related crystal structure.
