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The
Structurally Conserved Regions (SCRs)
are protein segments that conserve the same main-chain conformation
in all the three-dimensional structures analysed, excluding
the intervening regions whose structure differs markedly amongst
different proteins. The SCRs were presumably subjected to
similar constraints during the divergent evolution of a family
or superfamily of proteins from a common ancestor; therefore
they possibly contain most of the determinants necessary to
maintain the fold. SCR_FIND is a method for
the automatic identification of the SCRs, which assigns a
score for each position of a multiple structure alignment
based on the mean RMSD computed for the correspondent
coordinates of the structurally equivalent alpha carbons.
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Superimposition
of the SCRs found in PLP, fold type I enzymes.
The backbones of 23 superposed structures is shown as
solid oval ribbon. Seventeen regions with a mean positional
RMSD = 3.0 Å, lacking insertions and deletions
were detected and the corresponding coordinates coloured
according to the RMSD value. PLP is displayed as slate
CPKs. Oxygen atoms are coloured red, nitrogen atoms
blue, and phosphorus purple. |
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TUTORIAL |
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The
first thing you need to use SCR_FIND are two files,
one containing the superposed 3D structures of the
proteins being analysed, and the other containing
the corresponding residue multiple alignment. You
can find two examples of them clicking on the left.
If you want to write these files by yourself, please
follow these rules:
FILE WITH STRUCTURES:
It must be a standard
PDB file, with each different structure beginning
with "MODEL" and ending with "ENDMDL".
HETATMS are ignored, but they must be placed at the
end of each structure.
FILE WITH MULTIPLE ALIGNMENT:
It is a text file with a sequence for each line. The
header of each structure must have the following format:
pdb code:chain(lenght:first residue-last residue).
For example : 1BJ4:A(470:36-422).
Then the alignment.
Don't use the pdb code of a structure to rename these
files!
REMEMBER: there must be absolute correspondence between
protein sequence numbering in the two files.
For example, if the alignment of 1BJ4 starts with M36,
the corresponding structural coordinates MUST contain
MET 36, otherwise you could have problems!
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Alternatively,
you can download the files you need from the CE
site. Click on "Find
structural alignments by selecting from ALL"
and when the results are ready select the structures
you need and click on "GET ALIGNMENT".
Then, click on "Download alignment as a
PDB file" and "Download alignment
as text". Save these files on your hard-disk. |
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Upload
the files in the homepage of SCR_FIND.
In the following page modify the parameters required
to define a SCR.
Maximum RMSD value to define a SCR:
SCRs with a mean RMSD > than this value are not
considered.
Penalty for every gap foundPenalty for every
gap found:each time a gap is found in the
alignment, corresponding to an indel in the structure,
a penalty is added to the RMSD value.
Minimum residue lenght to define a SCR:
the minimum lenght to define a SCR.
Press SUBMIT to launch a new process.
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When
the results are ready, you can download your formatted
input files and a file ("SCR results")
with the score (mean RMSD + penalty for each gap found)
computed for every position of the alignment, and details
corcerning the SCRs found. Moreover, you can download
the 3D-COORDINATES OF THE SCRs and
the FASTA ALIGNMENT OF THE SCRs. Last,
you can VISUALIZE THE SCRS and the corresponding
alignment, both coloured according the mean and standard
deviation of the values found. |
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