An Efficient Null Model for Conformational Fluctuations in Proteins
(2012) In Structure 20(6). p.1028-1039- Abstract
- Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually,... (More)
- Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/2895932
- author
- Harder, Tim ; Borg, Mikael ; Bottaro, Sandro ; Boomsma, Wouter LU ; Olsson, Simon ; Ferkinghoff-Borg, Jesper and Hamelryck, Thomas
- organization
- publishing date
- 2012
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Structure
- volume
- 20
- issue
- 6
- pages
- 1028 - 1039
- publisher
- Cell Press
- external identifiers
-
- wos:000305094500011
- scopus:84861988477
- pmid:22578545
- ISSN
- 0969-2126
- DOI
- 10.1016/j.str.2012.03.020
- language
- English
- LU publication?
- yes
- id
- 0e149042-e7b7-4189-9183-5c6f513d43ca (old id 2895932)
- date added to LUP
- 2016-04-01 10:18:30
- date last changed
- 2024-01-06 13:26:39
@article{0e149042-e7b7-4189-9183-5c6f513d43ca,
abstract = {{Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins.}},
author = {{Harder, Tim and Borg, Mikael and Bottaro, Sandro and Boomsma, Wouter and Olsson, Simon and Ferkinghoff-Borg, Jesper and Hamelryck, Thomas}},
issn = {{0969-2126}},
language = {{eng}},
number = {{6}},
pages = {{1028--1039}},
publisher = {{Cell Press}},
series = {{Structure}},
title = {{An Efficient Null Model for Conformational Fluctuations in Proteins}},
url = {{https://lup.lub.lu.se/search/files/1732965/2970612.pdf}},
doi = {{10.1016/j.str.2012.03.020}},
volume = {{20}},
year = {{2012}},
}