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Landmark initialization consists of defining the initial coordinates and the initial covariance of landmarks (interest points).
The optimized structure for this species was used as a starting point for generating the initial coordinates for all other CDO models included in this study, with the appropriate atoms for the various adducts being added manually to this structure.
The initial coordinates for this system were taken from the crystallographic structure (PDB ID: 5L7C).
For the 14-3-3ε234-255 peptide simunfolded andunfoutspread outspread conformation was used as initial coordinates.
The initial state is chosen as where and are the initial coordinates of the object.
Taurolidine theoretical calculations were performed using initial coordinates from the corresponding X-ray molecular structure.
For the initial coordinates, the B chain was selected from 2QQR.
The initial coordinates were prepared the same as Roche et al. (33).
10.1186/s13068-015-0379-8 A file contheninitial initial coordinates for the simulation system for independent analysis.
Four independent replicas of unrestrained MD simulations were performed, starting from slightly different initial coordinates.
Initial coordinates were derived from conformer 1 of the cNTnC·Ca2+·Sp·bepridil NMR ensemble (PDB entry 1LXF).
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