PMC:2728203 / 30435-31350 JSONTXT

{"project":"2_test","denotations":[{"id":"18190927-8736557-62518000","span":{"begin":201,"end":203},"obj":"8736557"},{"id":"18190927-15312772-62518000","span":{"begin":201,"end":203},"obj":"15312772"}],"text":"Structures were calculated from polypeptide chains with randomized ϕ and ψ torsion angles using a two-stage simulated annealing protocol within the program XPLOR, essentially as described elsewhere,43,44 but employing larger numbers of cycles as follows: first-stage calculations comprised Powell energy minimization (500 steps), dynamics at 1000 K (25,000 steps), increase of the van der Waals force constant and tilting of the NOE potential function asymptote (4000 steps), switching to a square-well NOE function then cooling to 300 K in 2000 step cycles, and final Powell minimization (1000 steps). Second-stage calculations used Powell minimization (500 steps), increasing dihedral force constant during 4000 step cycles of dynamics at 1000 K (with a strong van der Waals force constant and square-well NOE potential function), cooling to 300 K in 1000 step cycles, and 2000 steps of final Powell minimization."}