Provides access to a number of circular dichroism secondary structure calculation algorithms and reference databases in a user-friendly manner. DICHROWEB accepts a wide range of data formats and units and provides a goodness-of-fit parameter for assessing the quality of the analyses and a range of tabular and graphical output formats of experimental, calculated and difference spectra.
A method for the secondary structure determination and fold recognition from protein circular dichroism spectra. BeStSel allows structural biologists to solve the secondary structure of their protein samples accurately and to gain more structural information. The versatile algorithm presents a significant improvement compared with existing ones. With fast CD spectral data acquisition and accurate structure determination, our algorithm provides biophysical scientists with a powerful tool.
Provides a means of identifying spectral nearest neighbours for an input query circular dichroism (CD) spectrum based on a reference data set of CD spectra. The default reference data set consists of the complete validated holdings of the PCDDB for which crystal structures are available. User-defined specialist reference data sets can also be used to generate results for specialized analyses, including for example, focusing on variations within the chosen protein group.
Provides a means of testing protein circular dichroism (CD) spectral data and metadata for quality, completeness and consistency, as well as identifying unusual but potentially important deviations from standard spectral characteristics. One of the primary aims for creating the ValiDichro server was to increase good practice within the field of protein CD spectroscopy, especially providing users with guidance regarding data quality. This is important, as CD is a complementary technique often used in conjunction with other structural biology methods by those who are not experts in its application. ValiDichro can be used as a valuable guide for data collection, as well as a test for data quality before publication, and as an indication to users of the data of its validity.
Predicts secondary structural content from a circular dichroism (CD) spectrum. K2D takes advantage of a recent notable development in the field of CD spectra estimation from structural data, DichroCalc, and of the high number of proteins in the Protein Data Bank (PDB), which covers a large range of structural configurations. When the size of the protein is included in the algorithm, K2D produces results comparable to other methods in terms of performance for the 190–240 nm interval and improves the performance for the 200–240 nm interval. K2D represents an improvement mostly in the predictions of beta-sheet content. Thus, we recommend using K2D if the size of the protein is known, especially if the CD spectrum is restricted to the 200 nm and up wavelength interval.
The 2Struc server provides two functionalities; 2Struc, which generates secondary structure element (SSE) assignments for protein structures for up to eight different methods enabling easy analyses of similarities and differences between them, and Compare-the-Protein, which allows comparisons and highlighting of differences between the SSEs generated within a series of NMR models or between two x-ray structures. 2Struc is unique in providing summaries of percentage secondary structure content for reduced three-state data and original SSE output assignments where generated.
A web interface that makes Circular dichroism (CD) and linear dichroism (LD) calculations available for the use of non-theoreticians, thus considerably improving the access to such calculations. Protein Data Bank (PDB) files can be processed by the hundreds and calculated spectra are sent to the user directly. The development of the interface spawned the Perl library ParsePDB.pm, which provides quick access to the parsed content of a PDB file in just one compact library.
A web server-based analysis tool for interpreting circular dichroism (CD) spectra. CAPITO allows the simultaneous evaluation of multiple datasets. Hence, it is suitable for the investigation of a protein in question under different conditions (temperature, pH, buffer solvent and mutations). Our approaches (basis spectra and matching-based method) to extract secondary structure information from a CD spectrum take advantage of a recent significant increase in the availability of well-calibrated far-UV CD spectra linked to available tertiary structures.
Produces circular dichroism spectra from protein atomic coordinate file. PDB2CD utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our data set.
Provides a simple way to analyse single or multiple circular dichroism (CD) spectra, resulting in data that can be applied in a quantitative form. CCA+ incorporates two CD spectrum analysis method: the LINCOMB (LINear COMBination of CD spectrum) and the CCA+ (Convex Constraint Analysis plus). The file import function can read directly the proprietary data file formats of the popular spectrometer software to make the analysis easier.
Provides an analytical approach to quantitative secondary structural information about quadruplexes from their measured CD spectra. Del Villar-GuerraEtAL2017 is an upon request algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental Circular dichroism (CD) spectra.
Predicts the electronic circular dichroism (CD) spectra of globular proteins from their model structures. SESCA refines and assesses protein model structures. It determines the model quality by comparing the proposed protein model to an experimentally determined CD spectrum. This software can also handle protein flexibility and contributions from amino acid side chains that enhance the accuracy of the method.
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