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Protein Folding Properties from Molecular Dynamics Simulations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. (Van der Spoel)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. (Van der Spoel)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. (Van der Spoel)
2007 (English)In: Applied Parallel Computing: State of the Art in Scientific Computing / [ed] Kagstrom B; Elmroth E; Dongarra J; Wasniewski J, 2007, p. 109-115Conference paper, Published paper (Refereed)
Abstract [en]

Protein folding simulations have contributed significantly to our understanding of the problem, since it is difficult to study individual molecules during the folding process. We have recently performed folding simulations of Chignolin, a decapeptide (Seibert et al., J. Mol. Biol. 354 (2006) p. 173) and introduced a new algorithm for deriving kinetics information as well as thermodynamics from the trajectories (Van der Spoel & Seibert, Phys. Rev. Lett. 96 (2006), p. 238102). Here we investigate the algorithm further and show that the folding reaction for Chignolin is a two-state folding reaction, in accord with experimental data.

Place, publisher, year, edition, pages
2007. p. 109-115
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 4699
National Category
Computer and Information Sciences Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-16718ISI: 000250904900013ISBN: 978-3-540-75754-2 (print)OAI: oai:DiVA.org:uu-16718DiVA, id: diva2:44489
Conference
8th International Workshop on Applied Parallel Computing (PARA 2006) Umea, SWEDEN, JUN 18-21, 2006
Available from: 2008-06-03 Created: 2008-06-03 Last updated: 2018-01-12Bibliographically approved

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Van Der Spoel, DavidPatriksson, AlexandraSeibert, Marvin

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