There are 7 reference sets (basis sets) in CDPro, and an 8th one can be created using CLUSTER program. These can be selected for analysis with any of the three softwares, SELCON3, CDSSTR and CONTINLL, by changing the IBasis (Basis_1) value in the INPUT file. [IBasis and Basis_1 are the same]
All these programs and the output can now be accessed with ease in a browser environment (Netscape navigator, 4.7, frames compatible). Place the files in C:/CDPro directory and open RunCDPro.html in Navigator.
IBasis
(Basis_1)Wavelength Range Number of Proteins Secondary Structures 1 178-260 nm 29 6 (aR, aD, bR, bD, T, U) 2 178-260 nm 22 6 (a, 3/10, b, T, P2, U) 3 185-240 nm 37 6 (aR, aD, bR, bD, T, U) 4 190-240 nm 43 6 (aR, aD, bR, bD, T, U) 5 185-240 nm 37* 5 (a, b, T, P2, U) 6 185-240 nm 42 6 (aR, aD, bR, bD, T, U) 7 190-240 nm 48 6 (aR, aD, bR, bD, T, U) 8 190-240 nm various 6 (aR, aD, bR, bD, T, U) List of proteins for IBasis = 3 and 5 are same; the secondary structure fractions are different -- option 3 splits the helix and sheet fractions, while option5 gives P2.
Results from IBasis values 1, 3, 4, 6 and 7 are comparable as the secondary structure fractions they estimate are identical (From DSSP assignments with regular and distorted helix and sheet structures). IBasis = 2 uses assignments from XTLSSTR program of King and Johnson and IBasis = 5 uses different types of structures from DSSP assignments (helix, sheet, turns, poly(Pro)II, and unordered) of secondary structure; results from these two options cannot be combined with those from others.
IBasis = 8 uses tertiary class specific protein set. Use CLUSTER to create the required files before using this option.To analyze your CD spectrum:
- Create INPUT file. Check that CD data is in per molar De units.
- Select the largest reference set that is available for the wavelength range of your CD data. For example, if your CD data is in the range 187-250 nm then the valid reference set has a wavelength range of 185-240 nm. The programs use CD spectra of reference proteins in the range 187-250 nm. You can select either 3 or 6 as your choice of IBasis (IBasis = 6 would select the reference set with both native and denatured proteins while IBasis = 3 would select the reference set with only native proteins).
- One could also use IBasis = 4 or 7, only in this case the CD data at wavelengths lower than 190 nm are not used in the analysis.
- With your choice of IBasis run the programs SELCON3, CDSSTR and CONTINLL (in any order) by clicking on the executable. This opens up a DOS window and runs the program. Check the outputs.
- Examine the ProtSS.OUT file for one solution from each program. The results from these programs for a given IBasis can be averaged.
- Calculated CD spectral data from the three programs are given in files: CalcCD.OUT (SELCON3), reconCD.OUT (CDSSTR), and CONTIN.CD (CONTINLL). Import these into a graphics program to compare the two. RMSD between the two is also output in ??????.OUT and ProtSS.out files.
- The results from two IBasis values can be averaged provided they correspond to the same types of secondary structures. (for example, IBasis= 3, 4, 6, and 7 give six secondary structures that are identical types and the results from them can be averaged.)
- Use CLUSTER to create the tertiary class specific reference protein set (cddata.ca and ssdata.ca). CLUSTER also modifies the INPUT file (IBasis=8). Subsequent execution of programs SELCON3, CDSSTR and CONTINLL (in any order) gives you solutions as described above.