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 |
|
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.
-
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)
-
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).
-
Save the file on your hard drive (or
diskette).