In crambin, the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.
Alignment quality was manually refined in the SeqLab (GCG, Wisconsin package) editor by moving residues.
FT-CORRECT-TRACE moves residues and FT-PERTURBATE-TRACE refines their mobility.
FT-CORRECT moves residues in the reconstructed 3D structure in order to decrease the difference between entries of the computed and input contact maps while preserving identical values.
Mainly, residues are not moved independently; since the graph topology has to be maintained, moving a residue involves moving all the residues positioned between it and a current cut point on its sequence.
The genes before the cut point χ are copied from one parent:, for i = 0, χ - 1; 2. For the second part of the offspring,, for i = χ, n - 1 unless this move forces residue i to overlap with one of the i - 1 previous ones.
This result supports our rotamer-based approach in the sense that residues that did not significantly move (rigid residues) are less prone to create or lose H-bonds than flexible residues.
This indicates that many of the latter residues move away from residues 77−79 on complex formation.
Additional refinements of the M antigen model were performed using a similar minimization protocol in which the type of residues constrained during the minimization were varied: initially, only residues out of the most favored regions of the Ramachandran plot were allowed to move, then residues with a high model B-factor and/or force field energy were included.
For a given propensity, each protein sequence is scanned using a sliding window, moved one residue at a time, starting from the N-terminus (protein profile).
Starting from the N-terminus of a protein, we use a sliding window of 21 amino acids that is moved one residue at a time until the C-terminus is reached.
