Input/Output Files for CDPro:
 
Program
Input File
Output Files / Contents
CLUSTER INPUT
1. CLUSTER.OUT  Summary output
2. INPUT  Modified INPUT file
SSDATA.CA
CDDATA.CA
Tertiary-class specific reference set
CDSSTR
INPUT
 1. CDSSTR.OUT Summary of CDSSTR output
 2. RECONCD.OUT CD spectra calculated and reconstructed
 3. PROTSS.OUT Final result appended to this file
SELCON3
INPUT
 1. SELCON3.OUT Summary of SELCON3 output
 2. CALACD.OUT CD spectra calculated 
 3. BASIS CD and SS data of refernece proteins
 4. PROTSS.OUT Final result appended to this file
CONTINLL
INPUT
 1. CONTINLL.OUT Summary of CONTINLL output
 2. CONTIN.OUT Original CONTIN output
 3. SUMMARY.PG Summary of each LL conbination
 4. BASIS.PG CD and SS data of refernece proteins
 5. PROTSS.OUT Final result appended to this file
 6. CONTIN.CD Calculated CD spectrum


Different Options (Reference Sets) Available in CDPro:
The reference set of proteins from different sources are combined to create a large reference set of 48 CD spectra. Depending on the wavelength range of interest the number of proteins in the reference set could be as large as 48. These are used in any of the three programs by changing the Basis_1 value (IBasis) in the INPUT file (varies from 1 to 7).

Results from IBasis values 1, 3, 4, 6 and 7 should be comparable as the secondary structure fractions they estimate are identical (Kabsch & Sander, 1983, DSSP assignments as modified by Sreerama et al). IBasis = 2 (King & Johnson, 1999) and IBasis = 5 (DSSP, as modified by Sreerama & Woody, 1994) use a different assignment of secondary structure.
IBasis = 8 uses tertiary class specific reference set that has to be created by executing program: CLUSTER.
 

IBasis
Wavelength Range
Proteins
References
Secondary Structures
1
178-260 nm
29
(Johnson et al.)
6 (aR, aD, bR, bD, T, U)
2
178-260 nm
22 
(Johnson)
6 (a, 3/10, b, T, P2, U)
3
185-240 nm
37 
(Johnson et al., Keiderling et al., & Sreerama et al.)
6 (aR, aD, bR, bD, T, U)
4
190-240 nm
43 
(Johnson et al., Keiderling et al., Yang et al., & Sreerama et al.)
6 (aR, aD, bR, bD, T, U)
5
185-240 nm
37 
(Johnson et al., Keiderling et al., & Sreerama et al.)
5 (a, b, T, P2, U)
6
185-240 nm
42 
(Johnson et al., Keiderling et al., & Sreerama et al.)
6 (aR, aD, bR, bD, T, U)
7
190-240 nm
48 
(Johnson et al., Keiderling et al., Yang et al., & Sreerama et al.)
6 (aR, aD, bR, bD, T, U)
8 190-240 nm Varies Tertiary Class Specific 6 (aR, aD, bR, bD, T, U)

 
 
Secondary structures Reference Proteins
a, a-Helix (AHel) 22, Johnson (22)
b, b-Sheet (BSht) 29, Johnson et al. (29)
aR, Regular a-Helix (Helix1, H(r)) 37, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5)
aD, Distorted a-Helix (Helix2, H(d)) 43, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5) + Yang et al. (6)
bR, Regular b-Strand (Strand1, S(r)) 42, Johnson et al (29) + Sreerama et al. (8) + Keiderling et al. (5)
bD, Distorted b-Strand (Sreand2, S(d)) 48, Johnson et al (29) + Sreerama et al. (8) + Keiderling et al. (5) + + Yang et al. (6)
3/10, 3/10 Helix 22, Johnson (22) 
P2, poly(Pro)II Structure 37, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5)
T, Turns
U, Unordered





Program and Data Files in CDPro:
Download Instructions:

These executables were created for an IBM-compatible PC. The SELCON3 and CONTINLL source codes can be compiled and used on any computer, but CDSSTR cannot be since it relies upon GetTim, Seed and Random routines of MSFortran. If CDSSTR source code for a unix machine is required please contact sreeram@lamar.colostate.edu

The files can be downloaded either individually or as a zip-file. The zip-file is: CDPro.zip(Double-Click on the name and save it on your PC. Copy it to the required directory and unzip it.)

It was created by PKZIP utility. If you donot have PKZIP utility you can download a freeware, command line version of pkzip25 from wuarchive.wustl.edu or download pk250c32.exe from this site (double-click on the name). Executing it on your computer creates the PKZIP25.EXE and instruction files. Command for unzipping the files is: PKZIP -extract CDPro.zip which implodes 42 files. The html files (index.htm, Guide.htm, Input.htm, Output.htm and CDPro.htm) have information about CDPro software.

One can also download each file separately if there is a problem or if PKUNZIP facility is not available, as instructed below.

  1. Create a directory ( C:/CDPRO if you want to use the RunCDPro.html from Netscape Navigator) in your computer hard drive (or insert a diskette in your floppy drive)
  2. Double-Click on the file names that are in columns Data Files, Source/Executable Code and Sample I/O files. This will either open a dialog box (for executables and large files) or bring the file in to the browser (select save option from file menu).
  3. Save the file on your hard drive (or diskette).
Data Files
CDDATA.29
SSDATA.29
CDDATA.23
SSDATA.23
CDDATA.37
SSDATA.37
CDDATA.43
SSDATA.43
CDDATA.P2
SSDATA.P2
CDDATA.42
SSDATA.42
CDDATA.48
SSDATA.48
CDDATA.AA
SSDATA.AA
CDDATA.AB
SSDATA.AB
CDDATA.BB
SSDATA.BB
plusalfa
slshalfa
slshplus
betaalfa
betaplus
betaslsh
dentalfa
dentplus
dentslsh
dentbeta
Software
Source/Executable Code
Sample I/O Files
CDSSTR CDSSTR.FOR
CDSSTR.EXE
 INPUT.SMP
CDSSTR.SMP
RECONCD.SMP
PROTSS.SMP
SELCON3 SELCON3.FOR
SELCON3.EXE
 INPUT.SMP
SELCON3.SMP
BASIS.SMP
CALCCD.SMP
PROTSS.SMP
CONTINLL CONTINLL.FOR
CONTINLL.EXE
 INPUT.SMP
CONTINLL.SMP
CONTIN.SMP
BASISPG.SMP
SUMMARY.SMP
PROTSS.SMP
CONTINCD.SMP
CRDATA CRDATA.FOR
CRDATA.EXE
CRDATA.INP
CRDATA.OUT
CLUSTER CLUSTER.FOR
CLUSTER.EXE
CLUSTER.SMP