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Table 9 Results of ten difficult cases of pairwise alignment

From: Protein structure search and local structure characterization

Protein 1 Protein 2 VAST DALI CE FATCAT Yang & Tung's de Brevern et al.'s Our SA
1fxia 1ubq 48(2.10) 60(2.60) 64(3.80) 63(3.01) 59(2.76) 76(2.89) 58(2.64)
1ten 3hhrb 78(1.60) 86(1.90) 87(1.90) 87(1.90) 57(2.57) 73(2.31) 90(2.24)
3hlab 2rhe_ - 63(2.50) 85(3.50) 79(2.81) 54(2.65) 78(3.01) 79(2.87)
2azaa 1paz_ 74(2.20) 81(2.50) 85(2.90) 87(3.01) 70(2.34) 57(2.23) 87(2.40)
1cewi 1mola 71(1.9) 81(2.30) 69(1.90) 83(2.44) 52(2.37) 53(2.35) 61(1.83)
1cid_ 2rhe_ 85(2.20) 95(3.30) 94(2.70) 100(3.11) 54(2.75) 53(2.49) 55(2.08)
1crl_ 1ede - 211(3.40) 187(3.20) 269(3.55) 167(3.35) 120(3.47) 187(3.25)
2sim_ 1nsba 284(3.80) 286(3.80) 264(3.00) 286(3.07) 121(2.75) 121(2.96) 137(3.2)
1bgea 2gmfa 74(2.50) 98(3.50) 94(4.10) 100(3.19) 27(3.34) 77(2.8) 78(2.72)
1tie_ 4fgf_ 82(1.70) 108(2.00) 116(2.90) 117(3.05) 91(3.15) 62(3.45) 115(3.05)
Average RMSD/aligned-residues   0.0226 0.0238 0.0261 0.0229 0.0373 0.0363 0.0278
  1. The number of residues aligned and the RMSD (in parentheses) are shown. The last row displays the average RMSD per aligned residue. Except for PBE-align, 3D-BLAST, and SA-FAST, the results of the methods were adopted from [36].