DEERconstruct

Version 2.2 (702 KB) von Thomas Casey

For testing suppressions in P(r) for Double Electron-Electron Resonance (DEER) spectroscopy data

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Aktualisiert 13. Mär 2020

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This App allows users to test the hypothesis that certain components of distance profiles obtained from fitting time domain Double Electron-Electron Resonance (DEER) data are insignificant and can be removed from consideration when deriving a physical meaning from the distance profile.

DEERconstruct accepts the output of DeerAnalysis or .dat files structured as follows:

(:,1) = distance axis
(:,2) = P(r)
(:,3) = time axis
(:,4) = zero time and background corrected time domain data
(:,5) = time domain fit corresponding to P(r)

The time domain signals are computed from each suppression combination using the typical dipolar kernel 'K(r,t)' and compared to the incoming P(r) by calculation of RMSD between their time domain representations.

Zitieren als

Casey, Thomas M., and Gail E. Fanucci. “Spin Labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease.” Methods in Enzymology, Elsevier, 2015, pp. 153–87, doi:10.1016/bs.mie.2015.07.019.

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Erstellt mit R2019b

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Version	Veröffentlicht	Versionshinweise
2.2	13. Mär 2020	-Minor layout adjustments	Herunterladen
2.1	24. Feb 2020	-Added option to revert an optimization if the results are illogical -Added back option to load the DeerAnalysis output. Select any of the _distr, _fit, etc.	Herunterladen
2.0	12. Feb 2020	-Transitioned to App Designer -Dramatically simplified interface and procedure -Removed all statistical inference, the RMSDs are given for each suppression combination -Input is now generic	Herunterladen
1.3	7. Nov 2019	- Pulled sub-functions out as separate m files - Use trapz functions instead of sum to get areas of populations - Updated my email address in the manual	Herunterladen
1.2.1.0	7. Jan 2016	-Minor bug fixes	Herunterladen
1.2.0.0	7. Jan 2016	-Saving now includes more of the original data and gives the option to save only the reports for qualified suppressions. -The distance profiles are now integral area normalized instead of amplitude normalized. -Updated manual.	Herunterladen
1.1.0.0	18. Sep 2015	-Fixed issue where filenames with multiple underscores didn't allow for the correct filename patching necessary for the code to find and load the "_fit" file -Added calculation of S/N.	Herunterladen
1.0.2.0	10. Sep 2015	minor code cleanup, minor bug fixes	Herunterladen
1.0.1.0	31. Jul 2015	-Removed {'fontname', 'symbol'} and replaced with call to latex interpreter for users with newer matlab versions -added zoom and data cursor buttons to the GUI	Herunterladen
1.0.0.0	6. Jul 2015		Herunterladen

MLA	Casey, Thomas M., and Gail E. Fanucci. “Spin Labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease.” Methods in Enzymology, Elsevier, 2015, pp. 153–87, doi:10.1016/bs.mie.2015.07.019.
APA	Casey, T. M., & Fanucci, G. E. (2015). Spin labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease. In Methods in Enzymology (pp. 153–187). Elsevier. Retrieved from https://doi.org/10.1016%2Fbs.mie.2015.07.019
BibTeX	@incollection{Casey_2015, doi = {10.1016/bs.mie.2015.07.019}, url = {https://doi.org/10.1016%2Fbs.mie.2015.07.019}, year = 2015, publisher = {Elsevier}, pages = {153--187}, author = {Thomas M. Casey and Gail E. Fanucci}, title = {Spin labeling and Double Electron-Electron Resonance ({DEER}) to Deconstruct Conformational Ensembles of {HIV} Protease}, booktitle = {Methods in Enzymology} }