Folding time predictions from all-atom replica exchange simulations
We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models.
| Medienart: |
Artikel |
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| Erscheinungsjahr: |
2007 |
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| Erschienen: |
2007 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:372 |
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| Enthalten in: |
Journal of molecular biology - 372(2007), 3 vom: 21. Sept., Seite 756-63 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Yang, Sichun [VerfasserIn] |
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| Themen: |
EC 3.6.1.- |
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| Anmerkungen: |
Date Completed 01.11.2007 Date Revised 03.09.2007 published: Print-Electronic Citation Status MEDLINE |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM171954084 |
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| 100 | 1 | |a Yang, Sichun |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Folding time predictions from all-atom replica exchange simulations |
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| 500 | |a Date Completed 01.11.2007 | ||
| 500 | |a Date Revised 03.09.2007 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
| 650 | 7 | |a GTP-Binding Proteins |2 NLM | |
| 650 | 7 | |a EC 3.6.1.- |2 NLM | |
| 700 | 1 | |a Onuchic, José N |e verfasserin |4 aut | |
| 700 | 1 | |a García, Angel E |e verfasserin |4 aut | |
| 700 | 1 | |a Levine, Herbert |e verfasserin |4 aut | |
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