Sampling Realistic Protein Conformations Using Local Structural Bias

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Standard

Sampling Realistic Protein Conformations Using Local Structural Bias. / Hamelryck, Thomas Wim; Kent, John T.; Krogh, A.

In: PLoS ONE, Vol. 2, No. 9, 2006, p. e131.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Hamelryck, TW, Kent, JT & Krogh, A 2006, 'Sampling Realistic Protein Conformations Using Local Structural Bias', PLoS ONE, vol. 2, no. 9, pp. e131. https://doi.org/10.1371/journal.pcbi.0020131

APA

Hamelryck, T. W., Kent, J. T., & Krogh, A. (2006). Sampling Realistic Protein Conformations Using Local Structural Bias. PLoS ONE, 2(9), e131. https://doi.org/10.1371/journal.pcbi.0020131

Vancouver

Hamelryck TW, Kent JT, Krogh A. Sampling Realistic Protein Conformations Using Local Structural Bias. PLoS ONE. 2006;2(9):e131. https://doi.org/10.1371/journal.pcbi.0020131

Author

Hamelryck, Thomas Wim ; Kent, John T. ; Krogh, A. / Sampling Realistic Protein Conformations Using Local Structural Bias. In: PLoS ONE. 2006 ; Vol. 2, No. 9. pp. e131.

Bibtex

@article{51f05be06c3711dcbee902004c4f4f50,
title = "Sampling Realistic Protein Conformations Using Local Structural Bias",
abstract = "The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design.",
author = "Hamelryck, {Thomas Wim} and Kent, {John T.} and A. Krogh",
year = "2006",
doi = "10.1371/journal.pcbi.0020131",
language = "English",
volume = "2",
pages = "e131",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

RIS

TY - JOUR

T1 - Sampling Realistic Protein Conformations Using Local Structural Bias

AU - Hamelryck, Thomas Wim

AU - Kent, John T.

AU - Krogh, A.

PY - 2006

Y1 - 2006

N2 - The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design.

AB - The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design.

U2 - 10.1371/journal.pcbi.0020131

DO - 10.1371/journal.pcbi.0020131

M3 - Journal article

VL - 2

SP - e131

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 9

ER -

ID: 1100863