rogram	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

The reference set of proteins from different sources are combined to create a large reference set of 56 CD spectra. Depending on the wavelength range of interest the number of proteins in the reference set could be as large as 56. These are used in any of the three programs by changing the IBasis value (formarly Basis_1) in the INPUT file (varies from 1 to 10).

Both SOLUBLE and MEMBRANE Proteins are now included in the reference set. Options 9 and 10 include 13 MEMBRANE proteins along with  37  and 43 soluble protiens, respectively, from options 3 and 4.

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	Reference Set	References	Secondary Structures
1	178-260 nm	29	SP29	(Johnson et al.)	6 (aR, aD, bR, bD, T, U)
2	178-260 nm	22	SP22X	(Johnson)	6 (a, 3/10, b, T, P2, U)
3	185-240 nm	37	SP37	(Johnson et al., Keiderling et al., & Sreerama et al.)	6 (aR, aD, bR, bD, T, U)
4	190-240 nm	43	SP43	(Johnson et al., Keiderling et al., Yang et al., & Sreerama et al.)	6 (aR, aD, bR, bD, T, U)
5	185-240 nm	37	SP37A	(Johnson et al., Keiderling et al., & Sreerama et al.)	5 (a, b, T, P2, U)
6	185-240 nm	42	SDP42	(Johnson et al., Keiderling et al., & Sreerama et al.)	6 (aR, aD, bR, bD, T, U)
7	190-240 nm	48	SDP48	(Johnson et al., Keiderling et al., Yang et al., & Sreerama et al.)	6 (aR, aD, bR, bD, T, U)
8	190-240 nm	Varies	CLSTR	Tertiary Class Specific	6 (aR, aD, bR, bD, T, U)
9	185-240 nm	50 (13 MP)	SMP50	(Johnson et al., Keiderling et al.,  Sreerama et al.& Park et al.)	6 (aR, aD, bR, bD, T, U)
10	190-240 nm	56 (13 MP)	SMP56	(Johnson et al., Keiderling et al., Yang et al.,  Sreerama et al. & Park et al.)	6 (aR, aD, bR, bD, T, U)

 
 

Secondary structures	Reference Proteins
a,a-Helix (AHel)	SP22X, Johnson (22)
b,b-Sheet (BSht)	SP29, Johnson et al. (29)
aR,Regulara-Helix (Helix1, H(r))	SP37, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5)
aD,Distorteda-Helix (Helix2, H(d))	SP43, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5) + Yang et al. (6)
bR,Regularb-Strand (Strand1, S(r))	SDP42, Johnson et al (29) + Sreerama et al. (8) + Keiderling et al. (5)
bD,Distortedb-Strand (Sreand2, S(d))	SDP48, Johnson et al (29) + Sreerama et al. (8) + Keiderling et al. (5) + + Yang et al. (6)
3/10, 3/10 Helix	SP37A, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5)
P2, poly(Pro)II Structure	SMP50,Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5)+ Park et al. (13)
T, Turns	SMP56, Johnson et al (29) + Sreerama et al. (3) + Keiderling et al. (5) + Yang et al. (6) + Park et al. (13)
U, Unordered

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. The CDSSTR source code for a unix machine is available. Other two programs run on unix machine as is (Just change the suffix from FOR to f; e.g., SELCON3.FOR to selcon3.f).

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 WINZIP utility. If you donot have WINZIP utility you can download it for free from INTERNET. Other softwares are also available for UNZIPPING the CDPro.zip file. If you have Windows XP, the XP operating system dows it for you. You can also use PKZIP25.EXE. 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, 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.50 SSDATA.50 CDDATA.56 SSDATA.56 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