ASH structure alignment package: Sensitivity and selectivity in domain classification
By Daron M. Standley, Hiroyuki Toh, Haruki Nakamura. 2007
43 citations recorded by the source corpus.
BackgroundStructure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/.ResultsThe new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC) curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure.ConclusionASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
- Kazutaka Katoh
- Daron M. Standley
- John Rozewicki
- Karlou Mar Amada
- Songling Li
- Akira R. Kinjo
- Haruki Nakamura
- Torsten Schwede
In Molecular Biology
- Daron M. Standley
- Kazutaka Katoh
- John Rozewicki
- Karlou Mar Amada
- Songling Li
- Akira R. Kinjo
- Haruki Nakamura
- B. Faircloth
Citations in the corpus
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “The residue-level equivalences, which form the basis of all ASH alignments, provide a convenient route for combining MAFFT and ASH.”
- MAFFT-DASH: integrated protein sequence and structural alignment (2019, methodology): “DASH is a stand-alone web-based database of pairwise structural alignments of representative PDB entries using the RASH structural alignment method (13).”
- Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format (2011, background): “org/ash (23,29,30) MAFTTash Integrated multiple sequence/structure alignment pdbj.”