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This page enables you to find the proteins in the pdb database
that have specific sheet motifs. The radio buttons have pre-selected
values that you can change by clicking around. You have to specify
the sequence of strands. You can also specify the strand orientations
(up or down), the loop lengths between the strands (long or short),
and the type of protein (all beta or alpha/beta). Those three
selections are optional, and you can omit them by clicking the
appropriate i don't care button. After you filled out the
form, click the execute button at the end of the page. If any of the
specified sheet motifs were found in the database, the standard 4
letter/digit abbreviation of the protein pdb file will be displayed.
Click on the Huh?s for help.
Specify the strand sequence:
Huh?
Select a position for each strand. You can not choose the same
position twice - it will give you an error on the output form! This
selection is optional - click the i don't care button to omit the
strand sequence.
| i don't care |
|
|
|
| strand 1 |
1
2
|
| strand 2 |
1
2
3
|
| strand 3 |
1
2
3
|
Select the orientation for each strand. 0 is up, 1 is down. This
selection is optional - click the i don't care button to omit the
strand orientations.
| i don't care |
|
|
|
| strand 1 |
0
|
| strand 2 |
0
1
|
| strand 3 |
0
1
|
Select the loop lengths between each pair of strands. 0 is short (10
residues or less), 1 is long (more than ten residues). This selection
is optional - click the i don't care button to omit the loop lengths.
| i don't care |
|
|
|
| loop 1 |
0
1
|
| loop 2 |
0
1
|
Select the type of the protein. alpha/beta are proteins with at least
20% of the residues in a helix, all beta proteins have less than 20%
of the residues in a helix. This selection is optional - click the i
don't care button (default) to omit the protein type.
|
i don't care
alpha/beta
all beta
|
Select the range for the number of amino acids in the domains or
proteins you want to allow.
residues minimum
residues maximum