title: Retrospective analysis of a secondary structure prediction: the catalytic domain of matrix metalloproteinases.
abstract: Secondary structure prediction of the catalytic domain of matrix metalloproteinases is evaluated in the light of recently published experimentally determined structures. The prediction was made by combining conformational propensity, surface probability, and residue conservation calculated for an alignment of 19 sequences. The position of each observed secondary structure element was correctly predicted with a high degree of accuracy, with a single beta-strand falsely predicted. The domain fold was also anticipated from the prediction by analogy with the structural elements found in the distantly related metalloproteinases thermolysin, astacin, and adamalysin.
authors.affiliation: British Bio-technology Limited, Oxford, United Kingdom.
authors.forename: E E
authors.initials: EE
authors.lastname: Hodgkin
authors.forename: I C
authors.initials: IC
authors.lastname: Gillman
authors.forename: R J
authors.initials: RJ
authors.lastname: Gilbert
mesh_terms: D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D017364:Collagenases / Q000737:chemistry; D006801:Humans; D019278:Matrix Metalloproteinase 3; D020783:Matrix Metalloproteinase 7; D008666:Metalloendopeptidases / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013025:Glycine max / Q000201:enzymology
chemical_list: D017364:Collagenases; D008666:Metalloendopeptidases; C024344:envelysin; D019278:Matrix Metalloproteinase 3; D020783:Matrix Metalloproteinase 7