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Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks.

Wei Zhang1, A Keith Dunker, Yaoqi Zhou

  • 1Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, USA.

Proteins
|October 13, 2007
PubMed
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Objective protein secondary structure assignment remains challenging. This study introduces a novel criterion using sequence-alignment benchmarks to evaluate six methods, finding STRIDE and KAKSI most accurate.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Objective assignment of protein secondary structures (helix, sheet, coil) is an unsolved problem.
  • Existing methods lack standard assignments, leading to arbitrary boundary definitions.

Purpose of the Study:

  • To propose and validate a novel criterion for objectively assessing protein secondary structure assignment methods.
  • To evaluate and rank six common secondary structure assignment algorithms.

Main Methods:

  • Developed a criterion based on the similarity of secondary structures in pairwise sequence-alignment benchmarks.
  • Benchmarks were derived from structural alignments of protein pairs.
  • Evaluated STRIDE, DSSP, SECSTR, KAKSI, P-SEA, and SEGNO using PREFAB, SABmark, and SALIGN benchmarks.

Related Experiment Videos

Main Results:

  • STRIDE and KAKSI demonstrated comparable and superior performance, achieving 1-4% higher success rates than other methods.
  • A consensus method (SKSP) combining STRIDE, KAKSI, SECSTR, and P-SEA further improved assignments by an additional 1%.

Conclusions:

  • Sequence-alignment benchmarks provide a useful means for evaluating secondary structure assignment methods.
  • The proposed criterion and the SKSP consensus method offer improved objective assessment of protein secondary structure assignments.