Table 3: The energy and RMSD values achieved by different algorithms using BM energy model. The bold-faced values indicate the winner. For both energy and RMSD values, the higher the better.

Protein sizeHybrid [12] Heuristics [13] ( ) Our GA ( )Our Rel. Imp.
and H-Count BM En RMSD BM En RMSD BM En RMSDRI w.r.t [13]
Seq Size H Best Avg Avg Best Avg Avg Best Avg Best Avg Energy RMSD

4RXN 5427−157.70−140.13 9.99−165.21−156.32 6.29 −166.88 −162.72 4.70 5.414.09%13.99%
1ENH 5419−154.24−141.9910.04 −168.75−146.69 6.61−153.79 −151.65 4.57 5.223.01%21.03%
4PTI 5832−213.70−196.2311.92 −219.52−198.42 7.07−210.29 −204.56 5.97 6.463.09%36.92%
2IGD 6125−184.29−157.2013.30 −187.20−174.19 9.33−183.18 −176.836.85 7.811.12%16.26%
1YPA 6438−221.11−208.1013.42−249.90−239.98 7.53 −256.95 −253.095.42 6.295.46%16.47%
1R69 6930−180.62−165.1114.78−213.04−204.17 6.47 −216.37 −208.794.68 5.172.26%20.09%
1CTF 7442−204.88−195.2312.65−224.29−213.81 7.23 −233.51 −225.434.69 5.285.43%26.97%

3MX7 9044−328.12−311.56 8.18 −340.05 −325.457.31 7.944.46%2.93%
3NBM 10856−418.60−401.99 8.58 −436.76 −419.255.58 6.464.29%24.71%
3MQO 12068−465.74−455.27 8.86 −486.05 −472.78 6.17 6.843.85%22.80%
3MRO 14263−445.33−430.2910.02 −479.36 −447.777.65 8.724.06%12.97%
3PNX 16084−601.23−571.13 9.38 −615.82 −592.25 7.50 8.513.70%9.28%