Search similar protein structures with classification, sequence and 3D alignments

Zaixin Lu, Zhiyu Zhao, Sergio Garcia, Krishnakumar Krishnaswamy, Bin Fu

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


We have developed an algorithm and web tool to search similar protein structures in the PDB (Protein Data Bank). The algorithm is a combination of a series of methods including protein classification, geometric feature extraction, sequence alignment, and 3D structure alignment. Given a protein structure, the tool can efficiently discover similar structures from hundreds of thousands of structures stored in the PDB. Our experimental results show that it is more accurate than other well-known protein search systems including PSI-BLAST, 3D-BLAST, and SSM in finding proteins that are structurally similar to the query protein, and its speed is also competitive with those systems. The algorithm has been fully implemented and is accessible online at the address, which is supported by a cluster of computers.

Original languageEnglish (US)
Pages (from-to)755-771
Number of pages17
JournalJournal of Bioinformatics and Computational Biology
Issue number5
StatePublished - 2009


  • Protein search
  • Protein structure alignment

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications


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