Table 2 Ranks of near-native structures using the optimised weighting factors
From: Optimised amino acid specific weighting factors for unbound protein docking
| Â | First structure with RMS<5Ã… in the ranking | Best structure with RMS<5Ã… in the ranking | ||||||
|---|---|---|---|---|---|---|---|---|
| Â | optimised | unoptimised | optimised | unoptimised | ||||
| Â | 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 |