DOI: 10.1073/pnas.0509355103. Physically realistic homology models built with <scp>rosetta</scp> can be more accurate than their templates

Physically realistic homology models built with rosetta can be more accurate than their templates

10.1073/pnas.0509355103

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

We have developed a method that combines the rosetta de novo protein folding and refinement protocol with distance constraints derived from homologous structures to build homology models that are frequently more accurate than their templates. We test this method by building complete-chain models for a benchmark set of 22 proteins, each with 1 or 2 candidate templates, for a total of 39 test cases. We use structure-based and sequence-based alignments for each of the test cases. All atoms, including hydrogens, are represented explicitly. The resulting models contain approximately the same number of atomic overlaps as experimentally determined crystal structures and maintain good stereochemistry. The most accurate models can be identified by their energies, and in 22 of 39 cases a model that is more accurate than the template over aligned regions is one of the 10 lowest-energy models.

Bibliography

Misura, K. M. S., Chivian, D., Rohl, C. A., Kim, D. E., & Baker, D. (2006). Physically realistic homology models built with rosetta can be more accurate than their templates. Proceedings of the National Academy of Sciences, 103(14), 5361â5366.

Authors 5

Kira M. S. Misura (first)
Dylan Chivian (additional)
Carol A. Rohl (additional)
David E. Kim (additional)
David Baker (additional)

References 23 Referenced 136

10.1146/annurev.biophys.29.1.291
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10.1002/prot.10529
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10.1073/pnas.95.19.11158
10.1002/prot.10557
10.1002/1097-0134(20010401)43:1<1::AID-PROT1012>3.0.CO;2-A
W. L. DeLano The pymol Molecular Graphics System (DeLano Scientific, San Carlos, CA, 2002). / The pymol Molecular Graphics System by DeLano W. L. (2002)

Dates

Type	When
Created	19 years, 4 months ago (March 27, 2006, 8:34 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 10:03 a.m.)
Indexed	1 year ago (Aug. 12, 2024, 7:51 a.m.)
Issued	19 years, 4 months ago (April 4, 2006)
Published	19 years, 4 months ago (April 4, 2006)
Published Online	19 years, 4 months ago (April 4, 2006)
Published Print	19 years, 4 months ago (April 4, 2006)

Funders 0

None

BibTeX

@article{Misura_2006, title={Physically realistic homology models built with <scp>rosetta</scp> can be more accurate than their templates}, volume={103}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0509355103}, DOI={10.1073/pnas.0509355103}, number={14}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Misura, Kira M. S. and Chivian, Dylan and Rohl, Carol A. and Kim, David E. and Baker, David}, year={2006}, month=apr, pages={5361–5366} }

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