Hamelryck, T., Kent, J.T. and Krogh, A. (2006) Sampling Realistic Protein Conformations Using Local Structural Bias. PLoS Computational Biology, 2 (9). e131. ISSN 1553-734X
Full text available as: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.
| Item Type: | Article |
|---|---|
| Copyright, Publisher and Additional Information: | © 2006 Hamelryck et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| Academic Units: | The University of Leeds > Faculty of Maths and Physical Sciences (Leeds) > School of Mathematics (Leeds) > Statistics (Leeds) |
| Depositing User: | Sherpa Assistant |
| Date Deposited: | 06 Nov 2009 12:07 |
| Last Modified: | 08 Feb 2013 17:07 |
| Published Version: | http://dx.doi.org/10.1371/journal.pcbi.0020131 |
| Status: | Published |
| Publisher: | Public Library of Science |
| Identification Number: | doi: 10.1371/journal.pcbi.0020131 |
| URI: | http://eprints.whiterose.ac.uk/id/eprint/10104 |
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