New local potential useful for genome annotation and 3D modeling
A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar (but not identical) to the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10 percent more structures correctly identified as the most likely structural match in a fold library, and 20 percent more structures correctly narrowed down to a set of five possible candidates. JThread also significantly improves the average sequence alignment accuracy, from 53 percent to 62 percent of residues correctly aligned. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- National Institute of Health under Contracts GM39900, F32-HG00200-03 and 1-P50-GM62412 (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 817247
- Report Number(s):
- LBNL-53557; JMOBAK; R&D Project: 864D1A; TRN: US200321%%341
- Journal Information:
- Journal of Molecular Biology, Vol. 233, Issue 4; Other Information: Journal Publication Date: 09/26/2003; PBD: 17 Jul 2003; ISSN 0022-2836
- Country of Publication:
- United States
- Language:
- English
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