Automated structure prediction of weakly homologous proteins on a genomic scale
Top Cited Papers
Open Access
- 4 May 2004
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 101 (20) , 7594-7599
- https://doi.org/10.1073/pnas.0305695101
Abstract
We have developed tasser, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement of continuous template fragments guided by an optimized Cα and side-chain-based potential driven by threading-based, predicted tertiary restraints. tasser was applied to a comprehensive benchmark set of 1,489 medium-sized proteins in the Protein Data Bank. With homologues excluded, in 927 cases, the templates identified by our threading algorithm prospector_3 have a rms deviation from native Escherichia coli genome; ≈920 can be predicted with high accuracy based on confidence criteria established in the Protein Data Bank benchmark. These results from our unprecedented comprehensive folding benchmark on all protein categories provide a reliable basis for the application of tasser to structural genomics, especially to proteins of low sequence identity to solved protein structures.Keywords
This publication has 30 references indexed in Scilit:
- Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein foldingProteins-Structure Function and Bioinformatics, 2002
- Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genomeProceedings of the National Academy of Sciences, 2002
- Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred foldsProteins-Structure Function and Bioinformatics, 2002
- GTOP: a database of protein structures predicted from genome sequencesNucleic Acids Research, 2002
- CDD: a database of conserved domain alignments with links to domain three-dimensional structureNucleic Acids Research, 2002
- Protein Structure Prediction and Structural GenomicsScience, 2001
- Prospects for ab initio protein structural genomicsJournal of Molecular Biology, 2001
- Structural genomics and its importance for gene function analysisNature Biotechnology, 2000
- Modeling of loops in protein structuresProtein Science, 2000
- The Protein Data BankNucleic Acids Research, 2000