A good TM score generally indicates that two protein structures have a similar overall shape or fold. Based on common benchmarks, a TM score higher than 0.5 suggests that two structures likely share the same fold.
Understanding the TM Score
The TM score is a metric used to quantify the structural similarity between two protein structures. It ranges from 0 to 1, where 1 indicates a perfect match between two structures (thus the higher the better).
Unlike older metrics that could be skewed by the size of the protein, the TM score is length-independent, making it a robust measure for comparing structures of different sizes.
Interpreting TM Score Values
The provided reference offers clear thresholds for interpreting TM scores:
- Scores below 0.20: According to the reference, scores below 0.20 correspond to randomly chosen unrelated proteins. This indicates virtually no significant structural similarity beyond what might be expected by chance.
- Scores higher than 0.5: Structures with a score higher than 0.5 assume roughly the same fold. This is the key threshold for identifying proteins with similar global structures.
This means that while scores between 0.20 and 0.5 might indicate some limited local similarity or perhaps a distant relationship, a score exceeding 0.5 is typically considered the benchmark for identifying homologous structures or structures belonging to the same fold family.
TM Score Interpretation Summary
Here's a simple way to summarize the interpretation based on the provided reference:
| TM Score Range | Interpretation | Structural Relationship |
|---|---|---|
| 0 - 0.20 | Very Low | Unrelated proteins (random similarity) |
| 0.20 - 0.50 | Moderate (may indicate some similarity) | Potential distant relationship or partial match |
| > 0.50 | Good (indicates same fold) | Roughly the same overall structure/fold |
| 1.0 | Perfect Match | Identical structures |
Therefore, when evaluating predicted or compared protein structures, a TM score significantly above 0.5 is considered indicative of a reliable structural match or prediction, reflecting the core definition of a "good" score in the context of protein fold similarity.
