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Native structure-based modeling and simulation of biomolecular systems per mouse click

Lutz, B.; Sinner, C.; Bozic, S.; Kondov, I.; Schug, A.


Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. ... mehr

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DOI: 10.5445/IR/1000046383
DOI: 10.1186/1471-2105-15-292
Zitationen: 2
Web of Science
Zitationen: 2
Cover der Publikation
Zugehörige Institution(en) am KIT Steinbuch Centre for Computing (SCC)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2014
Sprache Englisch
Identifikator ISSN: 1471-2105
KITopen-ID: 1000046383
HGF-Programm 46.04.19 (POF II, LK 01)
Erschienen in BMC Bioinformatics
Band 15
Heft 1
Seiten 292/1-12
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
Schlagwörter Protein folding; RNA folding; Native structure-based model; Molecular dynamics; GridBeans
Nachgewiesen in Web of Science
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