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Table 1 A comparison of the accuracy of the new scoring functions with other residue pair scoring functions from the literature in detecting correct threading solutions

From: Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

Residue pair scoring function

Rank 1

(0.02%)

Rank ≤ 50

(1%)

Rank ≤ 100

(5%)

1D

2357 (70.8%)

2945 (88.5%)

3030 (91.0%)

3D

2774 (83.4%)

3128 (94.0%)

3183 (95.6%)

6D

2911 (87.5%)

3200 (96.2%)

3231 (97.1%)

MJ1999

2714 (81.6%)

3033 (91.1%)

3068 (92.2%)

TE2000

2054 (61.7%)

2737 (82.2%)

2847 (85.5%)

RMF2006

623 (18.7%)

1632 (49.0%)

1906 (57.3%)

RMF2008/6-bin

1386 (41.6%)

2378 (71.5%)

2559 (76.9%)

RMF2008/7-bin

1396 (41.9%)

2391 (71.8%)

2548 (76.6%)

  1. The 5000 threading solutions for each of the 3328 template structures were ranked using either the 1D, 3D, or 6D residue pair scores or five different empirical potentials with available published parameters. The empirical potentials evaluated were from Miyazawa and Jernigan 1999 [16] (MJ1999), Tobi and Elber 2000 (TE2000), Rajgaria, McAllister, and Floudas 2006 [15] (RMF2006), and Rajgaria, McAllister, and Floudas 2008 [17] (RMF2008). The values indicate the number of protein structures for which the rank of the native sequence was within the indicated percentile. The corresponding percentage of the total structures is given in parentheses.
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BMC Bioinformatics

ISSN: 1471-2105

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