A Short Guide
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CDPro
software package consists of three of the popular programs (softwares)
for analyzing the protein CD spectra for determining the secondary
structure fractions (SELCON3, CDSSTR,and CONTIN) and a program for
determining tertiary structure class (CLUSTER). These programs can
now be run in a browser (Netscape
Navigator or Internet Explorer) environment with ease.The
program CONTIN has been
modified to include the variable selection of reference proteins in the
locally linearized model. The valid solutions from the variable
selection are selected using the new selection rule (Helix_Rule)
proposed by Johnson. This new selection rule is also incorporated in SELCON3.
One of the major problems in
using different programs for CD analysis has been the use of different
reference proteins and different assignments of secondary structures in
different softwares. The programs provided here have been modified to
accept any given set of reference proteins (CD spectra and secondary
structure fractions), and seven such reference sets (constructed from
the reference sets generally used in CD analysis) are provided. An
eighth set can be constructed based upon the tertiary structure class.
Moreover, input data files for these three programs are identical,
requiring the creation of a single input file (INPUT).
Estimates of alpha-helix,
bete-sheet, turns and poly(Pro)II secondary structures can be obtained
from CD analysis. Number of alpha-helical and beta-strand segments can
aso be estimated. Calculated CD spectral data (along with RMSD
and NRMSDwith
experimental data) from the three programs are output for easy
incorporation into a graphics software. RMSD and NRMSD from the three
programs decrease in the order:
SELCON3 > CDSSTR
> CONTINLL. (Use caution in
interpreting RMSDandNRMSD!)
Two new
reference sets, constructed by including membrane
proteins, are
also provided.
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