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Table 2 Constructed atomic structures for the skeletons in 1LRE: The structures are ranked by the contact energy (5th column), and those 32066 structures with negative contact energy are included in the table. The structure with the smallest RMSD to native (4.781 Å) is ranked the 17th.

From: Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures

Rank

Topology

Shift

Rot

CE

RMSD

1

123100

[-1, 1, 1]

[1.57, 1.57. 1.57]

-2.066887

7.224

2

123100

[-1, 1, -1]

[1.57, 1.57. 3.66]

-2.066817

7.517

...

...

...

...

...

...

17

123000

[1, 0, 1]

[5.76, 3.14, 1.57]

-2.004894

4.781

...

...

...

...

...

...

32066

123011

[1, -1, -1]

[1.05, 1.05, 0]

1.09E-4

12.979

  1. Rank: the rank of the structure by the contact energy (5th column)
  2. Topology: the topology Id, the 1st half of the digits: permutation of the assignment, the last half of the digits: directions (0 or 1) of the assignment for each helix;
  3. Shift: the amino acid position shift from the true helix segment for each assignment, "-" left, "+" right;
  4. Rot: rotation angle around the skeleton axis for each helix, in radian;
  5. CE: Effective contact energy of the constructed helices;
  6. RMSD: the root mean square deviation of the Cα atoms between the constructed candidate structure and the native structure, in Å.