Difference between revisions of "DASHA"
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The software DASHA is designed for the model-free analysis for NMR relaxation data. DASHA can be used as an optimisation engine to replace the minimisation algorithms implemented within relax. | The software DASHA is designed for the model-free analysis for NMR relaxation data. DASHA can be used as an optimisation engine to replace the minimisation algorithms implemented within relax. | ||
| − | == Website == | + | == Details == |
| + | |||
| + | === Website === | ||
The original DASHA website is http://www.nmr.ru/dasha.html (and [https://web.archive.org/web/20150223190004/http://www.nmr.ru/dasha.html archived on the Internet Archive]). | The original DASHA website is http://www.nmr.ru/dasha.html (and [https://web.archive.org/web/20150223190004/http://www.nmr.ru/dasha.html archived on the Internet Archive]). | ||
| − | == Overview == | + | === Overview === |
From the DASHA homepage: | From the DASHA homepage: | ||
| Line 11: | Line 13: | ||
{{quote|text=DASHA is an interactive program designed to investigate dynamics of biomolecules, for which data of <sup>15</sup>N or <sup>13</sup>C heteronuclear relaxation are available from NMR measurements. A number of sets of longitudinal and transverse relaxation rates of <sup>15</sup>N or <sup>13</sup>C nuclei and <sup>1</sup>H-<sup>15</sup>N, <sup>13</sup>C NOE's obtained at various NMR spectrometer frequencies might be used as the input. The measured longitudinal, transverse relaxation rates and NOE values are interpreted using the model-free approach of Lipari and Szabo (1982, J. Am. Chem. Soc., 104, 4546-4559). In addition to the overall rotational correlation time of the molecule, the internal dynamics of backbone N-H or C-H vectors of two types of internal motions - fast, on a time scale of <20 ps, and intermediate, close to 1 ns could be evaluated by constructing correspondent spectral density functions. Contribution of the conformational exchange to transverse relaxation rates of individual nitrogens or carbons could be elucidated using a set of different rates of the CPMG spin-lock pulse train in measuring {{:T2}} relaxation times (Orekhov et al., 1994, Eur. J. Biochem., 219, 887-896). Separate module DIFFC, included into the DASHA software, performs hydrodynamic calculations for proteins with known spatial structure. All input and output data could be easily presented in PostScript format.}} | {{quote|text=DASHA is an interactive program designed to investigate dynamics of biomolecules, for which data of <sup>15</sup>N or <sup>13</sup>C heteronuclear relaxation are available from NMR measurements. A number of sets of longitudinal and transverse relaxation rates of <sup>15</sup>N or <sup>13</sup>C nuclei and <sup>1</sup>H-<sup>15</sup>N, <sup>13</sup>C NOE's obtained at various NMR spectrometer frequencies might be used as the input. The measured longitudinal, transverse relaxation rates and NOE values are interpreted using the model-free approach of Lipari and Szabo (1982, J. Am. Chem. Soc., 104, 4546-4559). In addition to the overall rotational correlation time of the molecule, the internal dynamics of backbone N-H or C-H vectors of two types of internal motions - fast, on a time scale of <20 ps, and intermediate, close to 1 ns could be evaluated by constructing correspondent spectral density functions. Contribution of the conformational exchange to transverse relaxation rates of individual nitrogens or carbons could be elucidated using a set of different rates of the CPMG spin-lock pulse train in measuring {{:T2}} relaxation times (Orekhov et al., 1994, Eur. J. Biochem., 219, 887-896). Separate module DIFFC, included into the DASHA software, performs hydrodynamic calculations for proteins with known spatial structure. All input and output data could be easily presented in PostScript format.}} | ||
| − | == Authors == | + | === Authors === |
* Vladislav Yu. Orekhov | * Vladislav Yu. Orekhov | ||
| Line 19: | Line 21: | ||
* Alexander S. Arseniev. | * Alexander S. Arseniev. | ||
| − | == Version == | + | === Version === |
The last release was 3.48c in May 2000. | The last release was 3.48c in May 2000. | ||
| − | == Reference == | + | === Reference === |
* {{#lst:Citations|Orekhov95}} | * {{#lst:Citations|Orekhov95}} | ||
| + | |||
| + | == Usage in relax == | ||
| + | |||
| + | To use DASHA within relax, the following user function are provided: | ||
| + | |||
| + | * [http://www.nmr-relax.com/manual/dasha_create.html dasha.create] | ||
| + | * [http://www.nmr-relax.com/manual/dasha_execute.html dasha.execute] | ||
| + | * [http://www.nmr-relax.com/manual/dasha_extract.html dasha.extract] | ||
| + | |||
| + | These allow DASHA to be used as a model-free optimisation within relax, replacing the built-in algorithms. | ||
== See also == | == See also == | ||
[[Category:Model-free analysis]] | [[Category:Model-free analysis]] | ||
Revision as of 15:16, 15 December 2015
The software DASHA is designed for the model-free analysis for NMR relaxation data. DASHA can be used as an optimisation engine to replace the minimisation algorithms implemented within relax.
Contents
Details
Website
The original DASHA website is http://www.nmr.ru/dasha.html (and archived on the Internet Archive).
Overview
From the DASHA homepage:
| DASHA is an interactive program designed to investigate dynamics of biomolecules, for which data of 15N or 13C heteronuclear relaxation are available from NMR measurements. A number of sets of longitudinal and transverse relaxation rates of 15N or 13C nuclei and 1H-15N, 13C NOE's obtained at various NMR spectrometer frequencies might be used as the input. The measured longitudinal, transverse relaxation rates and NOE values are interpreted using the model-free approach of Lipari and Szabo (1982, J. Am. Chem. Soc., 104, 4546-4559). In addition to the overall rotational correlation time of the molecule, the internal dynamics of backbone N-H or C-H vectors of two types of internal motions - fast, on a time scale of <20 ps, and intermediate, close to 1 ns could be evaluated by constructing correspondent spectral density functions. Contribution of the conformational exchange to transverse relaxation rates of individual nitrogens or carbons could be elucidated using a set of different rates of the CPMG spin-lock pulse train in measuring T2 relaxation times (Orekhov et al., 1994, Eur. J. Biochem., 219, 887-896). Separate module DIFFC, included into the DASHA software, performs hydrodynamic calculations for proteins with known spatial structure. All input and output data could be easily presented in PostScript format. |
Authors
- Vladislav Yu. Orekhov
- Dmitry M. Korzhnev
- Dmitry E. Nolde
- Alexander P. Golovanov
- Alexander S. Arseniev.
Version
The last release was 3.48c in May 2000.
Reference
- Orekhov, V. Y., Nolde, D. E., Golovanov, A. P., Korzhnev, D. M. and Arseniev, A. S. (1995). Processing of heteronuclear NMR relaxation data with the new software DASHA Appl. Magn. Reson., 9(4), 581-588. (DOI: 10.1007/bf03162365)
Usage in relax
To use DASHA within relax, the following user function are provided:
These allow DASHA to be used as a model-free optimisation within relax, replacing the built-in algorithms.
