Structure-based function inference using protein family-specific fingerprints

Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


We describe a method to assign a protein structure to a functional family using family-specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active-site templates. Fingerprints were derived for 120 families in SCOP using Frequent Subgraph Mining. For a new structure, all occurrences of these family-specific fingerprints may be found by a fast algorithm for subgraph isomorphism; the structure can then be assigned to a family with a confidence value derived from the number of fingerprints found and their distribution in background proteins. In validation experiments, we infer the function of new members added to SCOP families and we discriminate between structurally similar, but functionally divergent TIM barrel families. We then apply our method to predict function for several structural genomics proteins, including orphan structures. Some predictions have been corroborated by other computational methods and some validated by subsequent functional characterization.

Original languageEnglish
Pages (from-to)1537-1543
Number of pages7
JournalProtein Science
Issue number6
StatePublished - Jun 2006


  • Almost-Delaunay
  • Delaunay
  • Orphan structures
  • Protein classification
  • Structural genomics
  • Structure-based function inference
  • Subgraph mining

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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