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 | + | The last release was {{current version DASHA}} 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]] | ||
| + | [[Category:Model-free software]] | ||
Latest revision as of 15:49, 21 October 2020
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.
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.