Protein structural alignments and functional genomics

James A. Irving, James C. Whisstock, Arthur M. Lesk

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


Structural genomics - the systematic solution of structures of the proteins of an organism - will increasingly often produce molecules of unknown function with no close relative of known function. Prediction of protein function from structure has thereby become a challenging problem of computational molecular biology. The strong conservation of active site conformations in homologous proteins suggests a method for identifying them. This depends on the relationship between size and goodness-of-fit of aligned substructures in homologous proteins. For all pairs of proteins studied, the root-mean-square deviation (RMSD) as a function of the number of residues aligned varies exponentially for large common substructures and linearly for small common substructures. The exponent of the dependence at large common substructures is well correlated with the RMSD of the core as originally calculated by Chothia and Lesk (EMBO J 1986;5:823-826), affording the possibility of reconciling different structural alignment procedures. In the region of small common substructures, reduced aligned subsets define active sites and can be used to suggest the locations of active sites in homologous proteins.

Original languageEnglish (US)
Pages (from-to)378-382
Number of pages5
JournalProteins: Structure, Function and Genetics
Issue number3
StatePublished - Feb 15 2001

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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