CDPro - Programs to Analyze Protein CD Spectra

CDPro software package consists of three of the popular programs (softwares) for analyzing the protein CD spectra for determining the secondary structure fractions (SELCON3, CDSSTR,and CONTIN) and a program for determining tertiary structure class (CLUSTER). The program CONTIN has been modified to include the variable selection of reference proteins in the locally linearized model. The valid solutions from the variable selection are selected using the new selection rule (Helix_Rule) proposed by Johnson. This new selection rule is also incorporated in SELCON3.

One of the major problems in using different programs for CD analysis has been the use of different reference proteins and different assignments of secondary structures in different softwares. The programs provided here have been modified to accept any given set of reference proteins (CD spectra and secondary structure fractions), and seven such reference sets (constructed from the reference sets generally used in CD analysis) are provided. An eighth set can be constructed based upon the tertiary structure class. Moreover, input data files for these three programs are identical, requiring the creation of a single input file (INPUT in CDPro). Two reference sets, constructed by including membrane proteins, are also provided.

Estimates of alpha-helix, beta-sheet, turns and poly(Pro)II secondary structures can be obtained from CD analysis. Number of alpha-helical and beta-strand segments can also be estimated. Calculated CD spectral data (along with RMSD and NRMSD with experimental data) from the three programs are output for easy incorporation into a graphics software. RMSD and NRMSD from the three programs decrease in the order: SELCON3 > CDSSTR > CONTINLL. (Use caution in interpreting RMSD and NRMSD!)

CDPro was initially written to be run in a browser interphase. But newer Operating Systems have enhanced security features, which do not allow running CDPro in a browser. These programs can be run in Batch Mode.