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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Saturating representation of loop conformational fragments in structure databanks
Narcis Fernandez-Fuentes1, András Fiser
1Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. narcis@fiserlab.org
BMC Structural Biology
|July 6, 2006
Summary
Protein structure prediction methods benefit from readily available protein loop fragments. Recent database expansion ensures dense coverage, meaning prediction is now limited by search algorithms, not fragment availability.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure prediction
Background:
- Short protein fragments are crucial for structure prediction, particularly in loop modeling and full structure assembly.
- The effectiveness of these methods relies heavily on the availability of diverse fragments in structural databases.
Purpose of the Study:
- To investigate the representation and coverage of protein loop fragments up to 14 residues in sequence and structure databases.
- To assess the relationship between sequence identity and structural similarity for protein loop fragments.
Main Methods:
- Clustering of all possible protein loop fragments from sequence databases (Sequence Space).
- Cross-referencing clustered sequence fragments with structural fragments in the Protein Data Bank (Structure Space).
- Analysis of sequence identity thresholds for structural similarity.
Main Results:
- The Protein Data Bank (PDB) expansion has led to dense coverage of loop conformational fragments.
- For loop fragments of length 8, at least one structure with >= 50% sequence identity exists in the PDB.
- Coverage decreases for longer loops, but all fragments up to 14 residues have matches with >= 20% sequence identity.
Conclusions:
- Fragment-based prediction is no longer limited by fragment availability but by the efficiency of search and scoring algorithms.
- Ongoing efforts like the Protein Structure Initiative will further enhance structure space coverage, improving prediction capabilities.
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