Coarse graining biomolecular systems
Lund, Mikael LU
(2007)
8th International Workshop on Applied Parallel Computing, PARA 2006
In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
4699 LNCS.
p.73-81
- Abstract
Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple "mesoscopic" protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants of... (More)
Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple "mesoscopic" protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants of proteins.
(Less)
- author
- Lund, Mikael
LU
- publishing date
- 2007
- type
- Chapter in Book/Report/Conference proceeding
- publication status
- published
- subject
- host publication
- Applied Parallel Computing. State of the Art in Scientific Computing : 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers - 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers
- series title
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
- editor
- Kågström, Bo ; Elmroth, Erik ; Dongarra, Jack and Waśniewski, Jerzy
- volume
- 4699 LNCS
- pages
- 9 pages
- publisher
- Springer
- conference name
- 8th International Workshop on Applied Parallel Computing, PARA 2006
- conference location
- Umea, Sweden
- conference dates
- 2007-06-18 - 2007-06-21
- external identifiers
-
- scopus:38049091693
- ISSN
- 1611-3349
- 0302-9743
- ISBN
- 9783540757542
- DOI
- 10.1007/978-3-540-75755-9_9
- language
- English
- LU publication?
- no
- id
- ab5b709a-deb9-484c-9be1-b65382639f79
- date added to LUP
- 2021-11-12 13:08:59
- date last changed
- 2024-04-26 02:21:23
@inproceedings{ab5b709a-deb9-484c-9be1-b65382639f79,
abstract = {{<p>Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple "mesoscopic" protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants of proteins.</p>}},
author = {{Lund, Mikael}},
booktitle = {{Applied Parallel Computing. State of the Art in Scientific Computing : 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers}},
editor = {{Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Waśniewski, Jerzy}},
isbn = {{9783540757542}},
issn = {{1611-3349}},
language = {{eng}},
pages = {{73--81}},
publisher = {{Springer}},
series = {{Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}},
title = {{Coarse graining biomolecular systems}},
url = {{http://dx.doi.org/10.1007/978-3-540-75755-9_9}},
doi = {{10.1007/978-3-540-75755-9_9}},
volume = {{4699 LNCS}},
year = {{2007}},
}