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.
Predicts secondary structure fractions of a protein from its circular dichroism (CD) spectrum. K2D is a public web platform, leaning on a k-nearest neighbor (k-NN) approach, that uses a database of theoretically derived CD spectra from the whole PDB repository. This program can be used for evaluating the alpha helix and beta-strand contents of a protein. The third version of the software especially focuses on the analysis of spectra restricted to the 200 nm and up wavelength interval.
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.
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.
Assists users in handling of structural and biophysical problems. PCSB is a package that has several applications, such as peptide parameter calculation, automatization of circular dichroism (CD) data processing or fluorescence data processing, alignement of three-dimensional structures, calculation of rotation axes, searching of anomalous scattering factors, symmetry operations or calculation of the Matthews coefficient.
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.
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.