DOI: 10.1073/pnas.022408799. Improved recognition of native-like protein structures using a family of designed sequences

Improved recognition of native-like protein structures using a family of designed sequences

10.1073/pnas.022408799

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The goal of the inverse protein folding problem is to identify amino acid sequences that stabilize a given target protein conformation. Methods that attempt to solve this problem have proven useful for protein sequence design. Here we show that the same methods can provide valuable information for protein fold recognition and for ab initio protein structure prediction. We present a measure of the compatibility of a test sequence with a target model structure, based on computational protein design. The model structure is used as input to design a family of low free energy sequences, and these sequences are compared with the test sequence by using a metric in sequence space based on nearest-neighbor connectivity. We find that this measure is able to recognize the native fold of a myoglobin sequence among different globin folds. It is also powerful enough to recognize near-native protein structures among nonnative models.

Bibliography

Koehl, P., & Levitt, M. (2002). Improved recognition of native-like protein structures using a family of designed sequences. Proceedings of the National Academy of Sciences, 99(2), 691â696.

Authors 2

Patrice Koehl (first)
Michael Levitt (additional)

References 51 Referenced 13

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:36 a.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 9:03 a.m.)
Indexed	1 year, 5 months ago (March 13, 2024, 9:44 a.m.)
Issued	23 years, 7 months ago (Jan. 8, 2002)
Published	23 years, 7 months ago (Jan. 8, 2002)
Published Online	23 years, 7 months ago (Jan. 8, 2002)
Published Print	23 years, 7 months ago (Jan. 22, 2002)

Funders 0

None

BibTeX

@article{Koehl_2002, title={Improved recognition of native-like protein structures using a family of designed sequences}, volume={99}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.022408799}, DOI={10.1073/pnas.022408799}, number={2}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Koehl, Patrice and Levitt, Michael}, year={2002}, month=jan, pages={691–696} }

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