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Table 2 Ranks of near-native structures using the optimised weighting factors

From: Optimised amino acid specific weighting factors for unbound protein docking

  First structure with RMS<5Å in the ranking Best structure with RMS<5Å in the ranking
  optimised unoptimised optimised unoptimised
  Rank RMS Rank RMS Rank RMS Rank RMS
EI
1ACB 3 2.638 19 0.934 91 0.934 19 0.934
1AVW 200 4.864 1024 2.978 2684 1.591 31428 1.591
1BRC 15 4.564 10 4.373 3118 1.019 27685 1.019
1BRS 5 1.966 35 4.685 5 1.966 22544 1.966
1BVN 2332 4.416 116 3.978 4118 1.718 15554 1.718
1CGI 31 4.295 57 4.616 922 1.659 27836 1.659
1CHO 1 2.779 63 0.809 171 0.809 63 0.809
1CSE 4334 4.791 414 3.526 9756 0.614 5831 0.614
1DFJ 532 4.145 6441 4.145 5182 3.869 17621 3.869
1FSS 149 4.098 228 1.621 467 1.092 966 1.092
1MAH 94 2.442 380 4.878 508 1.183 840 1.183
1PPF 9 4.351 37 4.593 242 2.457 23526 2.457
1TGS 2 1.97 59 3.366 848 0.849 169 0.849
1UGH 13 2.672 45 3.031 33 2.023 17059 2.023
2KAI 18 3.959 1 4.873 1387 1.316 28310 1.316
2MTA 374 4.64 110 4.743 3704 1.111 32445 1.111
2PCB 881 4.419 1803 4.419 11627 3.184 26851 3.184
2PCC 2548 4.125 1122 2.885 24009 2.885 1122 2.885
2PTC 20 4.572 558 4.428 8695 1.439 11164 1.439
2SNI 59 3.733 538 4.63 2701 2.814 3803 2.814
OTH
1AVZ 19685 3.964 7706 3.964 20034 3.891 11460 3.891
1BDJ 2216 4.552 7 2.799 39913 1.986 9733 1.986
1L0Y 839 2.271 4103 4.747 19996 1.627 29097 1.627
1WQ1 305 2.756 6 4.75 608 1.711 23213 1.711
AA
1AHW 580 4.766 143 1.943 620 1.07 4722 1.07
1DQJ 1066 3.966 6580 3.966 1066 3.966 6580 3.966
1VFB 323 4.894 3706 4.683 2763 1.481 35146 1.481
1WEJ 304 4.025 11382 4.025 789 0.917 34658 0.917