Studying Protein Clefts in Comparative Models
Author Information
Author(s): David Piedra, Sergi Lois, Xavier de la Cruz
Primary Institution: Institut de Recerca Biomèdica
Hypothesis
How does the preservation of protein clefts vary in homology models based on sequence identity?
Conclusion
The study shows that cleft quality in homology models varies significantly with sequence identity, indicating that good models can be found even at low sequence identities.
Supporting Evidence
- The study found that cleft quality improves with higher sequence identity.
- Good models can be identified even at low sequence identities (20%-30%).
- Proper identification methods can recover good cleft models in low sequence identity ranges.
Takeaway
This study looks at how well the important parts of proteins, called clefts, are preserved when we create models of them. It finds that even when the proteins are not very similar, we can still get good models.
Methodology
The study analyzed 53507 homology models using six parameters related to cleft quality and sequence identity.
Limitations
The study primarily focuses on the largest cleft and may not fully represent the quality of smaller clefts.
Digital Object Identifier (DOI)
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