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

(2009) BMC Bioinformatics 10 Suppl 1

PubMed: 19208142 | PubMedCentral: PMC2648730 | DOI: 10.1186/1471-2105-10-S1-S40

Figure 4 Top 100 structures for the skeletons in 1LRE (PDB Id) .

This approach was able to rank the most near native structure at the 17 th of 32066, the 16 th of 98755, the 5 th of 192935 and the 31 st of 391833 structures for 1LRE , 1DP3A , 1GXGA , and 1JW2A respectively (Table 3 ).

Table 2 shows an example (PDB Id = 1LRE ) of the ranked structures for the skeletons.

Table 2 Constructed atomic structures for the skeletons in 1LRE : The structures are ranked by the contact energy (5 th column), and those 32066 structures with negative contact energy are included in the table.

Protein Assignments Rank Topology Shift Rot CE RMSD 1LRE 32066 17 123000 [1, 0, 1] [5.76, 3.14, 1.57] -2.004894 4.781 1JW2A 391833 31 12340000 [-1, -1, 1, 0] [0, 0, 3.66, 5.76] -1.751024 4.718 1DP3A 98755 16 123000 [-1, 0, -1] [4.71, 5.23, 1.05] -2.414033 4.341 1GXGA 192935 5 124000 [-1, 0, 1] [5.23, 3.66, 2.09] -2.784552 4.665 Protein: the PDB Id; Assignments: the total number of assignments with the negative contact energy Rank: the rank of the structure with the smallest RMSD to native; Topology: the topology Id, the 1 st half of the digits: permutation of the assignment, the last half of the digits: directions (0 or 1) of the assignment for each helix; Shift: the amino acid position shift from the true helix segment for each assignment, "-" left, "+" right; Rot: rotation angle around the skeleton axis for each helix, in radian; CE: Effective contact energy of the constructed helices; RMSD: the root mean square deviation of the C α atoms between the constructed candidate structure and the native structure, in Å.

The structures of the skeleton of 1LRE were ranked by the contact energy of the secondary structures (top penal of Figure 4 ).

Publication Year: 2009