Table 1.
Summary of systems used to evaluate scoring functions. Those shown in bold were used in the PMF calculations.
| System (PDB ID) | Residues and Chainsa | IRMSD Range of Docking Resultsb |
Number of Poses Tested |
Reference |
|---|---|---|---|---|
| Ubiquitin ligase and ubiquitin (2OOB) |
Total: 113 Pull: 42 Stationary: 71 |
1.62Å–9.97Å | 96 | 7 |
| Trypsin and CMTI-I peptide inhbitor (1PPE) |
Total: 274 Pull: 29 Stationary: 245 |
0.65Å–9.67Å | 100 | 8 |
|
Antibody and antigen (1VFB) |
Total: 352 Pull: 129 Stationary: 107 & 116 |
1.32Å–9.98Å | 100 | 9 |
|
aminoacyl-tRNA synthetase and tRNA aminoacylation cofactor Arc1p (2HRK) |
Total: 282 Pull: 102 Stationary: 180 |
1.96Å–9.94Å | 98 | 10 |
| Ribonuclease A and a peptide inhibitor (1DFJ) |
Total : 579 Pull: 124 Stationary: 455 |
1.19Å–9.81Å | 99 | 11 |
| Ferredoxin-NADP Reductase and ferredoxin (1EWY) |
Total: 395 Pull: 98 Stationary:297 |
1.43 Å–9.98 Å | 100 | 12 |
| Matriptase and aprotinin (1EAW) |
Total: 299 Pull:58 Stationary: 241 |
0.74 Å –9.89 Å | 100 | 13 |
| SARS-receptor binding domain and receptor (2AJF) |
Total: 777 Pull:180 Stationary:597 |
1.63Å–10.0 Å | 98 | 14 |
| Ecotin and trypsin (1EZU) |
Total:365 Pull:142 Stationary:223 |
1.37 Å – 9.99 Å | 97 | 15 |
| Uracil-DNA Glycosylase and its protein inhibitor (1UDI) |
Total:207 Pull:83 Stationary: 124 |
1.15 Å – 9.89 Å | 100 | 16 |
a
“Pull” refers to the length of the chain that was pulled during the steered MD simulation, “Stationary” refers to the chain that was restrained during the steered MD simulation.
b
Results were pre-filtered to remove any poses above 10 Å.