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Targeting novel folds for structural genomics

McGuffin, LJ; Jones, DT; (2002) Targeting novel folds for structural genomics. PROTEINS , 48 (1) 44 - 52. 10.1002/prot.10129.

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Abstract

The ultimate goal of structural genomics is to obtain the structure of each protein coded by each gene within a genome to determine gene function. Because of cost and time limitations, it remains impractical to solve the structure for every gene product experimentally. Up to a point, reasonably accurate three-dimensional structures can be deduced for proteins with homologous sequences by using comparative modeling. Beyond this, fold recognition or threading methods can be used for proteins showing little homology to any known fold, although this is relatively time-consuming and limited by the library of template folds currently available. Therefore, it is appropriate to develop methods that can increase our knowledge base, expanding our fold libraries by earmarking potentially "novel" folds for experimental structure determination. How can we sift through proteomic data rapidly and yet reliably identify novel folds as targets for structural genomics? We have analyzed a number of simple methods that discriminate between "novel" and "known" folds. We propose that simple alignments of secondary structure elements using predicted secondary structure could potentially be a more selective method than both a simple fold recognition method (GenTHREADER) and standard sequence alignment at finding novel folds when sequences show no detectable homology to proteins with known structures. (C) 2002 Wiley-Liss, Inc.

Type:Article
Title:Targeting novel folds for structural genomics
DOI:10.1002/prot.10129
Keywords:secondary structure alignment, sequence alignment, amino acid composition, fold recognition, PROTEIN SECONDARY STRUCTURE, PREDICTION, RECOGNITION, CLASSIFICATION, SEQUENCES, MATRICES, SCOP, CATH
UCL classification:UCL > School of BEAMS > Faculty of Engineering Science > Computer Science

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