DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data

2004 | Lee Whitmore and B. A. Wallace
DICHROWEB is an online web server for analyzing circular dichroism (CD) spectroscopic data to determine protein secondary structure. It provides calculated secondary structure content and graphical comparisons between calculated and experimental data. The server is accessible via a password-protected user ID, obtained after completing a registration form. It supports a wide range of input formats, including those from commercial CD instruments and synchrotron radiation-based CD beamlines, as well as data from spectral processing software. The server uses five popular algorithms and seven reference databases to perform deconvolution analyses. It produces calculated secondary structures, a goodness-of-fit parameter, and tabular and graphical displays of experimental, calculated, and difference spectra. The server also provides information on CD methods, literature references, and aids for interpreting results. The server supports various input formats, including data from Aviv, Jasco, and Applied Photophysics CD software, Daresbury SRCD data format, Brookhaven SRCD data format, and a 'free' format. It accepts data in units of delta epsilon, mean residue ellipticity, theta, or SRCD counts. The user can select a low wavelength cut-off to exclude data with poor signal-to-noise ratios. Seven reference datasets are available, each requiring different wavelength ranges. The server also allows for optional scaling of spectra due to potential errors in protein concentration or instrument calibration. The output includes a summary of the best deconvolution, a detailed report with fit parameters, and graphical outputs of experimental and calculated spectra. The NRMSD (normalized root mean square deviation) is a goodness-of-fit parameter that measures the correspondence between experimental and calculated spectra. The server provides results in common CD units and can be used as a conversion tool. It also includes information pages, FAQs, and a user guide. Future developments include a membrane-protein CD reference database, a new soluble protein reference database, and the ability to select user-defined reference databases. The server is freely available to academic and non-profit organizations. DICHROWEB facilitates access to CD deconvolution algorithms regardless of data source, units, or file structure. It is a user-friendly tool for analyzing CD spectroscopic data to determine protein secondary structure.DICHROWEB is an online web server for analyzing circular dichroism (CD) spectroscopic data to determine protein secondary structure. It provides calculated secondary structure content and graphical comparisons between calculated and experimental data. The server is accessible via a password-protected user ID, obtained after completing a registration form. It supports a wide range of input formats, including those from commercial CD instruments and synchrotron radiation-based CD beamlines, as well as data from spectral processing software. The server uses five popular algorithms and seven reference databases to perform deconvolution analyses. It produces calculated secondary structures, a goodness-of-fit parameter, and tabular and graphical displays of experimental, calculated, and difference spectra. The server also provides information on CD methods, literature references, and aids for interpreting results. The server supports various input formats, including data from Aviv, Jasco, and Applied Photophysics CD software, Daresbury SRCD data format, Brookhaven SRCD data format, and a 'free' format. It accepts data in units of delta epsilon, mean residue ellipticity, theta, or SRCD counts. The user can select a low wavelength cut-off to exclude data with poor signal-to-noise ratios. Seven reference datasets are available, each requiring different wavelength ranges. The server also allows for optional scaling of spectra due to potential errors in protein concentration or instrument calibration. The output includes a summary of the best deconvolution, a detailed report with fit parameters, and graphical outputs of experimental and calculated spectra. The NRMSD (normalized root mean square deviation) is a goodness-of-fit parameter that measures the correspondence between experimental and calculated spectra. The server provides results in common CD units and can be used as a conversion tool. It also includes information pages, FAQs, and a user guide. Future developments include a membrane-protein CD reference database, a new soluble protein reference database, and the ability to select user-defined reference databases. The server is freely available to academic and non-profit organizations. DICHROWEB facilitates access to CD deconvolution algorithms regardless of data source, units, or file structure. It is a user-friendly tool for analyzing CD spectroscopic data to determine protein secondary structure.
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