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CCRXP ADV
CCRXP Lite
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Example output
Enter a valid four-letter PDB ID:
CCR XP Examples
Example 1
Example 2
CCR XP derived images (clusters in graphics)
Example 1
Example 2
Citations
CCRs in DNA-binding proteins
CCR XP method
CCRXP ADV: User selected parameters for CCR identification
Choose a critereon to determine residue positions in space (from all atom coordinates to single atom position)
For calculating packing density:
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C-alpha atom
Geometric center of all residue atoms
For clustering residues:
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C-alpha atom
Geometric center of all residue atoms
Choose a distance critereon, at which residues will be included in packing density calculations and clustering
For calculating packing density (number of residues within the following distance):
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7A
8.0A
9.0
10.0
For clustering residues (two residues will be joined if they are closer than the following distance):
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4.0A
4.5A
5.0A
5.5A
6.0A
6.5A
Definition of residue contact with DNA (any to any atom distance) (has no effect for structures without DNA molecule).
3.0A
3.5A
4.0A
4.5A
5.0A
5.5A
6.0A
6.5A
-->
Conservation score options:
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1. Maximum number of aligned sequences:
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20
50
100
150
200
Conservation score cutoff to include in clustering:
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0.5
0.6
0.7
0.8
0.9
Other filtering options:
Include only exposed residues in clustering at following relative ASA cutoff (% exposed units):
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0 (include all residues)
10
20
30
40
50
Minimum number of residues in a cluster (clusters smaller than this will not be reported)
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1
2
3
4
5
Enter a valid 4-letter PDB ID of your protein (leave blank if a file is uploaded)
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Upload your PDB file in the following: