Molecular nonlinear dynamics and protein thermal uncertainty quantification
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stabili...
| Main Authors: | , |
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| Format: | Journal Article |
| Language: | English |
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2016
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| Online Access: | https://hdl.handle.net/10356/82121 http://hdl.handle.net/10220/41112 |
| _version_ | 1826126748033482752 |
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| author | Xia, Kelin Wei, Guo-Wei |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Xia, Kelin Wei, Guo-Wei |
| author_sort | Xia, Kelin |
| collection | NTU |
| description | This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. |
| first_indexed | 2024-10-01T06:57:45Z |
| format | Journal Article |
| id | ntu-10356/82121 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:57:45Z |
| publishDate | 2016 |
| record_format | dspace |
| spelling | ntu-10356/821212023-02-28T19:32:30Z Molecular nonlinear dynamics and protein thermal uncertainty quantification Xia, Kelin Wei, Guo-Wei School of Physical and Mathematical Sciences Proteins Protein folding This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. Published version 2016-08-10T04:49:31Z 2019-12-06T14:47:05Z 2016-08-10T04:49:31Z 2019-12-06T14:47:05Z 2014 Journal Article Xia, K., & Wei, G.-W. (2014). Molecular nonlinear dynamics and protein thermal uncertainty quantification. Chaos, 24(1), 013103-. 1054-1500 https://hdl.handle.net/10356/82121 http://hdl.handle.net/10220/41112 10.1063/1.4861202 24697365 en Chaos © 2014 American Institute of Physics. This paper was published in Chaos and is made available as an electronic reprint (preprint) with permission of American Institute of Physics. The published version is available at: [http://dx.doi.org/10.1063/1.4861202]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. 12 p. application/pdf |
| spellingShingle | Proteins Protein folding Xia, Kelin Wei, Guo-Wei Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title | Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title_full | Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title_fullStr | Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title_full_unstemmed | Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title_short | Molecular nonlinear dynamics and protein thermal uncertainty quantification |
| title_sort | molecular nonlinear dynamics and protein thermal uncertainty quantification |
| topic | Proteins Protein folding |
| url | https://hdl.handle.net/10356/82121 http://hdl.handle.net/10220/41112 |
| work_keys_str_mv | AT xiakelin molecularnonlineardynamicsandproteinthermaluncertaintyquantification AT weiguowei molecularnonlineardynamicsandproteinthermaluncertaintyquantification |