Understanding Protein Loop Fragments in Databanks
Author Information
Author(s): Fernandez-Fuentes Narcis, Fiser András
Primary Institution: Albert Einstein College of Medicine
Hypothesis
What fraction of loops extracted from all known protein sequences is covered by loops extracted from all known protein structures?
Conclusion
The study suggests that fragment-based prediction approaches are now limited by the effectiveness of scoring and search algorithms rather than the completeness of fragments in databanks.
Supporting Evidence
- The expansion of the Protein Data Bank has resulted in a dense coverage of loop conformational fragments.
- For loops of length 8, there is at least one matching loop in the structure space with 50% or higher sequence identity.
- The study found that the number of unique sequence segments increased about six-fold over five years.
Takeaway
Scientists looked at how well short pieces of proteins are represented in databases, finding that there are enough pieces available to help build accurate models of protein structures.
Methodology
The study involved clustering and cross-referencing protein loop fragments from sequence databases with structural fragments in the Protein Data Bank.
Limitations
The study primarily focused on loops of lengths 8 to 14 residues and may not represent all protein fragments.
Digital Object Identifier (DOI)
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