| NMR | Nuclear Magnetic Resonance |
| CPU | Central Processing Unit |
| GPU | graphics processing unit |
| Cryo-EM | cryo-electron microscopy |
| PDB | Protein Data Bank |
| CASP | Critical Assessment of techniques for Structure Prediction |
| CHARMM | Chemistry at Harvard Macromolecular Mechanics |
| SVM | Support Vector Machine |
| NAMD | Nanoscale Molecular Dynamics |
| LDDT | Local Distance Difference Test on All Atoms |
| TBM | Template-Based Modelling |
| FM | Free Modelling |
| MQAPs | Model Quality Assessment Programs |
| MD | Molecular Dynamics |
| DFIRE | Distance-Scaled, Finite-Ideal Gas Reference |
| DDFIRE | Dipolar Distance-Scaled, Ideal Gas Reference |
| RWplus | Random Walk reference state Plus |
| GDT-TS | Global Distance Test Total Score |
| GDT_HA | Global Distance Test High Accuracy |
| SphGr | SphereGrinder |
| RMSD | Root mean square deviation |
| TM-Score | Template Modeling Score |