Opinion Progress towards mapping the universe of protein folds Alastair Grant, David Lee and Christine Orengo Address: Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK. Correspondence: Alastair Grant. E-mail: grant@ comment Published: 29 April 2004 reviews Genome Biology 2004, 5:107 The electronic version of this article is the complete one and can be found online at © 2004 BioMed Central Ltd Abstract Although the precise aims differ between the various international structural genomics initiatives currently aiming to illuminate the universe of protein folds, many selectively target protein families for which the fold is unknown. How well can the current set. | Opinion Progress towards mapping the universe of protein folds Alastair Grant David Lee and Christine Orengo Address Department of Biochemistry and Molecular Biology University College Gower Street London WC1E 6BT UK. Correspondence Alastair Grant. E-mail grant@ Published 29 April 2004 Genome Biology 2004 5 107 The electronic version of this article is the complete one and can be found online at http 2004 5 5 107 2004 BioMed Central Ltd Abstract Although the precise aims differ between the various international structural genomics initiatives currently aiming to illuminate the universe of protein folds many selectively target protein families for which the fold is unknown. How well can the current set of known protein families and folds be used to estimate the total number of folds in nature and will structural genomics initiatives yield representatives for all the major protein families within a reasonable time scale In order to attempt predictions of the universe of protein folds - so-called fold space - we need to know how many protein families there are in nature and how many of these are likely to possess a novel fold. Genome sequencing still considerably outpaces the various structural genomics initiatives currently underway in the USA Canada Japan Germany and the UK with more than 160 completely sequenced genomes yielding about one million protein sequences at the start of 2004 1 . This contrasts with 24 000 entries of three-dimensional protein structures in the Protein Data Bank PDB 2 3 some 500 of which were determined by structural genomics consortia over the last three years. Although this seems a daunting contrast mounting evidence from the Gene3D our unpublished data and 4 SUPERFAMILY 5 6 and Genomic Threading 7 8 databases suggests that a relatively small repertoire of protein folds around 800 can already be mapped onto about half of all the amino-acid residues encoded in the currently available genome sequences. .
