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Please cite the following:
Optimizing protein backbone torsion angles during structure refinement. *(unpublished) Haipeng Gong, Xiaojing Yang, Abhishek K. Jha, Joe DeBartolo, Kent W. Mouw, Phoebe A. Rice, Tobin R. Sosnick and Karl F. Freed
Upload initial Structure A in PDB format:
Enter final Structure B:
Enter chain ID and the range of residues (by index number) to undergo dihedral angle moves (e.g. "A,22,33" = move residues 22-33 on Chain A, put each range on a separate line, and use chain ID = A if none exists):
Enter chain ID and range of residues (by index number) whose final positions should match reference structure (enter same as above, but not yet fully implemented):
Choose movetype: . φ,ψ noise level (in degrees) =
Sample ω angle: noise level (in degrees) =
Pathway of PDB files: Save structures every (0.1 Å minimum) change in RMSD
Energy terms (leave alone if unfamiliar)
Reference similarity: Tors Stat Pot (w/NN effects): Tors Stat Pot: Steric overlap: Hbond: DOPE-PW: DOPE-PW Energy terms (leave alone if unfamiliar) EE (local): HH (local): CC (local): EE (antiparallel): EE (parallel): 0A: 1A: 2A: Simulated Annealing terms (leave alone if unfamiliar) MAX TEMP INIT STEPS: MAX TEMP ACCEPT RATIO: TEMP UPDATE INTERVAL: DEFAULT INIT TEMP: SMOOTH DEVIATION COEFFICIENT: UPDATE TEMP COEFFICIENT: TEMP CONVERGENCE COEFFICIENT:CALCULATE INIT TEMP: CHECK TEMP CONVERGENCE: LOCAL MINIMIZATION:
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