Feedback algorithm and web-server for protein structure alignment.

Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa

Research output: Contribution to journalArticlepeer-review


We have developed a feedback algorithm for protein structure alignment between two protein backbones. A web portal implementing this method has been constructed and is freely available for use at with a mirror site at We compare our algorithm with three other, commonly used methods: CE, DaliLite and SSM. The results show that in most cases our algorithm outputs a larger number of aligned positions when the (Calpha) RMSD is comparable. Also, in many cases where the number of aligned positions is larger or comparable, our learning method is able to achieve a smaller (Calpha) RMSD than the other methods tested. This trend of larger number of aligned positions and smaller (Calpha) RMSD is observed more frequently in cases where the similarity between protein structures is weak.

Original languageEnglish (US)
Pages (from-to)109-120
Number of pages12
JournalComputational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
StatePublished - 2008

ASJC Scopus subject areas

  • Medicine(all)


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