Computing ensembles of transitions from stable states : Dynamic importance sampling
Copyright © 2010 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 32(2011), 2 vom: 30. Jan., Seite 196-209 |
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| Weitere Verfasser: | , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2011
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Calcium-Binding Proteins Cell Cycle Proteins G-substrate Monosaccharide Transport Proteins Nerve Tissue Proteins Periplasmic Binding Proteins Polysaccharides Proteins S100 Calcium Binding Protein A6 mehr... |
| Zusammenfassung: | Copyright © 2010 Wiley Periodicals, Inc. There is an increasing dataset of solved biomolecular structures in more than one conformation and increasing evidence that large-scale conformational change is critical for biomolecular function. In this article, we present our implementation of a dynamic importance sampling (DIMS) algorithm that is directed toward improving our understanding of important intermediate states between experimentally defined starting and ending points. This complements traditional molecular dynamics methods where most of the sampling time is spent in the stable free energy wells defined by these initial and final points. As such, the algorithm creates a candidate set of transitions that provide insights for the much slower and probably most important, functionally relevant degrees of freedom. The method is implemented in the program CHARMM and is tested on six systems of growing size and complexity. These systems, the folding of Protein A and of Protein G, the conformational changes in the calcium sensor S100A6, the glucose-galactose-binding protein, maltodextrin, and lactoferrin, are also compared against other approaches that have been suggested in the literature. The results suggest good sampling on a diverse set of intermediates for all six systems with an ability to control the bias and thus to sample distributions of trajectories for the analysis of intermediate states |
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| Beschreibung: | Date Completed 25.03.2011 Date Revised 19.07.2024 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.21564 |