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Efficient Monte Carlo trial moves for polypeptide simulations
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View: Figures


Image of FIG. 1.
FIG. 1.

Fixed end move (FEM) description. The white circles represent the atoms rotating around the axis by an angle . The black circles represent the fixed atoms.

Image of FIG. 2.
FIG. 2.

Generalized coordinates of the end residue involved in a segment rotation. , and are the backbone bond unit vectors, , and are backbone bond angles, and and are the backbone dihedral angles.

Image of FIG. 3.
FIG. 3.

Example of conformation space density along a rotation trajectory. The density is shown for all values without imposing any restrictions on the bond angles. This particular example corresponds to a window size of nine residues.

Image of FIG. 4.
FIG. 4.

Fractional folding time in Monte Carlo steps for a group of 33 different proteins (dots). The fractional folding time corresponds to the time it takes 2 out of 40 independent folding simulations to reach the native state, starting from random unfolded structures. The solid line correspond to a power-law interpolation, given by . The PDB code for the proteins are: 1ptq, 1mhn-A, 1d0d-A, 1vie, 1ctf, 1ail, 1utg, 1cc8-A, 1bdo, 1blu, 1ctj, 1f60-B, 1l5p-C, 1plc, 1k5n-B, 1kte, 1m8n-D, 1jf8A, 1h3q-A, 1c3m-A, 1f08-B, 1amx, 1iv3-F, 1gui-A, 1jtg-D, 1lry-A, 1aqb, 1ex2-B, 1etp-B, 1ka9-H, 1mbm-D, 1gen, and 1iqq-A.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Efficient Monte Carlo trial moves for polypeptide simulations