There are 10 reference sets (basis sets) in CDPro, and of these one (IBasis = 8) is 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]
IBasis = 9 and 10 combine 13-MEMBRANE PROTEINS with 37- and 43-SOLUBLE proteins
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.
It also works in IE6.0 on a NT operating system.
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) 9 185-240 nm 50 (37 SP and 13 MP)
6 (aR, aD, bR, bD, T, U) 10
190-240 nm 56 (43 SP and 13 MP) 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, and 9 and 10, 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 (and, 9 & 10) 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.