SPalign / SPalign-NS
SPalign is a program that optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding.
SPalign-NS: Non-sequential Protein Structure Alignment
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Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.
Brown P, Pullan W, Yang Y, Zhou Y.
Bioinformatics. 2015 Oct 10. pii: btv580.
Proteins. 2012 Aug;80(8):2080-8. doi: 10.1002/prot.24100. Epub 2012 May 25.
A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction.
Yang Y1, Zhan J, Zhao H, Zhou Y.