Table 2.
The minimum RMSDs between the bioactive conformations and the structures from the different computer-generated datasets
| Ligand | omega a | nmrclust b | rms c | rms_avg d | Ligand | omega a | nmrclust b | rms c | rms_avg d |
|---|---|---|---|---|---|---|---|---|---|
| 1CIM | 1.199 | 1.199 | 1.199 | 1.199 | 1UVT | 1.315 | 1.329 | 1.296 | 1.315 |
| 1QPE | 0.775 | 0.775 | 0.736 | 0.775 | 1YDT | 1.104 | 1.154 | 1.154 | 1.154 |
| 1YDR | 0.932 | 0.932 | 0.932 | 0.932 | 2CGR | 1.087 | 1.087 | 1.659 | 1.613 |
| 2PCP | 1.14 | 1.14 | 1.14 | 1.14 | 3ERT | 0.384 | 0.569 | 0.472 | 0.738 |
| 1F4E | 0.787 | 0.787 | 1.019 | 0.801 | 1M48 | 1.315 | 1.41 | 1.658 | 1.678 |
| 1FCX | 0.761 | 0.81 | 0.871 | 0.81 | 1NHU | 1.267 | 1.458 | 1.458 | 1.458 |
| 1H1P | 0.493 | 0.681 | 0.708 | 0.708 | 1NHV | 1.227 | 1.227 | 1.051 | 1.051 |
| 1H9U | 0.766 | 1 | 0.772 | 0.772 | 2QWI | 1.035 | 1.114 | 1.082 | 1.106 |
| 1 JSV | 1.049 | 1.229 | 1.229 | 1.229 | 1K1 J | 1.528 | 1.528 | 1.528 | 1.528 |
| 1BR6 | 0.6 | 0.751 | 0.6 | 0.6 | 1KV2 | 2.163 | 2.118 | 2.167 | 2.143 |
| 1DLR | 0.164 | 0.164 | 0.599 | 0.599 | 1MQ6 | 0.991 | 1.177 | 1.197 | 1.23 |
| 1FCZ | 1.083 | 1.105 | 1.114 | 1.114 | 7DFR | 1.654 | 1.851 | 0.929 | 1.455 |
| 1L2S | 0.533 | 0.738 | 1.033 | 0.935 | 1EZQ | 0.871 | 0.953 | 1.054 | 1.116 |
| 2CSN | 0.267 | 0.33 | 0.267 | 0.267 | 1FKG | 1.639 | 1.66 | 1.118 | 1.413 |
| 1K7E | 0.857 | 0.977 | 0.796 | 1.113 | 1K22 | 1.02 | 1.02 | 1.224 | 1.224 |
| 1KV1 | 0.435 | 0.435 | 0.63 | 0.8 | 1QBU | 1.241 | 1.453 | 1.509 | 1.446 |
| 1QL9 | 0.836 | 1.018 | 1.064 | 0.98 | 1HFC | 1.018 | 1.306 | 1.386 | 1.047 |
| 1YDS | 0.951 | 1.058 | 1.008 | 1.065 | 1MNC | 0.572 | 1.057 | 1.152 | 1.152 |
| 5STD | 0.314 | 0.586 | 1.351 | 1.663 | 1OHR | 1.174 | 1.298 | 1.298 | 1.298 |
| 1EVE | 0.394 | 0.467 | 0.969 | 1.082 | 1UVS | 1.483 | 1.541 | 1.541 | 1.541 |
| 1F0T | 0.933 | 1.13 | 1.204 | 0.932 | 7EST | 1.25 | 1.475 | 1.371 | 1.393 |
| 1H1S | 0.839 | 0.839 | 1.153 | 1.231 | 1ELA | 0.892 | 0.892 | 0.945 | 1.108 |
| 1HDQ | 0.766 | 0.766 | 0.788 | 1.099 | 1GWX | 1.375 | 1.375 | 1.375 | 1.375 |
| 1K7F | 0.715 | 0.715 | 0.807 | 0.807 | 1HPV | 1.094 | 1.094 | 1.733 | 1.136 |
| 1A42 | 0.907 | 0.951 | 0.937 | 1.012 | 1O86 | 0.885 | 1.05 | 1.205 | 1.205 |
| 1IF7 | 0.334 | 0.534 | 0.941 | 0.657 | 1F4G | 1.266 | 1.304 | 1.367 | 1.367 |
| 1L8G | 1.44 | 1.44 | 1.361 | 1.361 | 1HTF | 1.284 | 1.395 | 1.395 | 1.256 |
| 1LQD | 0.724 | 0.992 | 1.138 | 0.726 | 1MMB | 0.915 | 0.915 | 0.915 | 0.915 |
| 966C | 1.41 | 1.525 | 1.625 | 1.625 | Average | 0.973 | 1.068 | 1.127 | 1.131 |
It can be seen that the bioactive conformer is present when a smaller ensemble size is employed
aEnumerated with recommended settings in OMEGA
Generated by: b Clustering the OMEGA conformers employing the NMRCLUST algorithm
cAdjusting the rms parameter of OMEGA to generate similar numbers of conformers as the number of clusters identified by the NMRCLUST algorithm
dPartitioning the dataset into low, medium and large numbers of rotatable bonds, averaging the rms values in each group and using the averaged rms values