Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods Changhoon Kim and BK Lee Laboratory of Molecular Biology CCR/NCI/NIH.

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Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods Changhoon Kim and BK Lee Laboratory of Molecular Biology CCR/NCI/NIH

What we did … Evaluated 7 structure alignment programs selected based on their availability and popularity (CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA, VAST) Standard of truth: NCBI’s CDD alignments Conserved Domain Database is manually procured. Contains only the conserved core residues. Performance Measure

Average fraction of correctly aligned residues (Average FCAR) Maximum allowed shift error

Sequence similarity dependence of Average FCAR(0) Average FCAR(0) Number of superfamilies Sequence similarity (% identity)

Variation of fCAR for individual structure pairs Correctly aligned fractions (fCAR) Alignments sorted by fCAR(0) within each superfamily

An example of alignment errors CDD alignment CE alignment DaliLite alignment