| UPS | ubiquitin-proteasome system |
| RPs | regulatory particles |
| CP | core particle |
| PCD | protein conformational disorders |
| ChT-L | chymotrypsin-like |
| T-L | trypsin-like |
| C-L | caspase-like |
| IDP | intrinsically disordered proteins |
| h20S | human 20S |
| y20S | yeast 20S |
| SARs | structure–activity relationships |
| STD | saturation transfer difference |
| WL | WaterLogsy |
| SA | simulated annealing |
| MM | molecular mechanics |
| RMSD | root mean square deviation |