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Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance.
1Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551, USA. venclovas@llnl.gov
Proteins
|October 28, 2003
Summary
The fifth Critical Assessment of protein Structure Prediction (CASP5) showed improved protein structure modeling, particularly for distant homology. Enhancements in template use and alignment accuracy were noted, though some errors persist in unreliable regions.
Area of Science:
- Structural biology
- Computational biology
- Bioinformatics
Background:
- The Critical Assessment of protein Structure Prediction (CASP) is a community-wide experiment to assess protein structure prediction methods.
- CASP5 involved "blind" testing of models for 20 comparative modeling targets, building upon methods used in CASP4.
Purpose of the Study:
- To evaluate the performance of protein structure prediction methods in CASP5.
- To identify improvements and persistent challenges in comparative modeling, especially for distant homology.
Main Methods:
- Utilized multiple templates for model building.
- Assessed alignment reliability in a region-specific manner.
- Employed structure-based selection of alignment variants in unreliable regions.
Main Results:
- CASP5 demonstrated significant improvements over CASP4, particularly in distant homology modeling.
- More effective use of multiple templates and enhanced alignment accuracy were key improvements.
- Misalignments in structurally conserved regions occurred primarily in unreliable regions, often lacking conserved sequence patterns.
Conclusions:
- Comparative modeling is expanding to more distant evolutionary relationships.
- Further development of sensitive energy-based methods is needed for challenging regions.
- Protein structure prediction continues to advance, aiding in the characterization of protein sequences.