Coarse graining biomolecular systems

Mikael Lund

doi:10.1007/978-3-540-75755-9_9

Coarse graining biomolecular systems

Mikael Lund

Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic

Research output: Chapter in Book/Report/Conference proceeding › Paper in conference proceeding › peer-review

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 proteins.

Original language	English
Title of host publication	Applied Parallel Computing. State of the Art in Scientific Computing
Subtitle of host publication	8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers
Editors/authors	Bo Kågström, Erik Elmroth, Jack Dongarra, Jerzy Waśniewski
Publisher	Springer
Pages	73-81
Number of pages	9
ISBN (Print)	9783540757542
DOIs	https://doi.org/10.1007/978-3-540-75755-9_9
Publication status	Published - 2007
Externally published	Yes
Event	8th International Workshop on Applied Parallel Computing, PARA 2006 - Umea, Sweden Duration: 2007 Jun 18 → 2007 Jun 21

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4699 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	8th International Workshop on Applied Parallel Computing, PARA 2006
Country/Territory	Sweden
City	Umea
Period	2007/06/18 → 2007/06/21

Subject classification (UKÄ)

Theoretical Chemistry (including Computational Chemistry)

Access to Document

10.1007/978-3-540-75755-9_9

Cite this

Lund, M. (2007). Coarse graining biomolecular systems. In B. Kågström, E. Elmroth, J. Dongarra, & J. Waśniewski (Eds.), Applied Parallel Computing. State of the Art in Scientific Computing: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers (pp. 73-81). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4699 LNCS). Springer. https://doi.org/10.1007/978-3-540-75755-9_9

Lund, Mikael. / Coarse graining biomolecular systems. 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 / Bo Kågström ; Erik Elmroth ; Jack Dongarra ; Jerzy Waśniewski. Springer, 2007. pp. 73-81 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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 proteins.",

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Lund, M 2007, Coarse graining biomolecular systems. in B Kågström, E Elmroth, J Dongarra & J Waśniewski (eds), Applied Parallel Computing. State of the Art in Scientific Computing: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4699 LNCS, Springer, pp. 73-81, 8th International Workshop on Applied Parallel Computing, PARA 2006, Umea, Sweden, 2007/06/18. https://doi.org/10.1007/978-3-540-75755-9_9

Coarse graining biomolecular systems. / Lund, Mikael.
Applied Parallel Computing. State of the Art in Scientific Computing: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers. ed. / Bo Kågström; Erik Elmroth; Jack Dongarra; Jerzy Waśniewski. Springer, 2007. p. 73-81 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4699 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Paper in conference proceeding › peer-review

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N2 - 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.

AB - 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.

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DO - 10.1007/978-3-540-75755-9_9

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Applied Parallel Computing. State of the Art in Scientific Computing

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T2 - 8th International Workshop on Applied Parallel Computing, PARA 2006

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Lund M. Coarse graining biomolecular systems. In Kågström B, Elmroth E, Dongarra J, Waśniewski J, editors, Applied Parallel Computing. State of the Art in Scientific Computing: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers. Springer. 2007. p. 73-81. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-75755-9_9

Coarse graining biomolecular systems

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