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iRMSD-APDB
Evaluates Multiple Sequence Alignment using structural information with APDB and iRMSD.
Alignment input
Paste or upload your Multiple Sequence Alignment in CLUSTAL format.
Alignment
Click here to use the sample file
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Click here to upload a file
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Srad - the Sphere Radius
APDB is a local method and the structural neighbourhood of each residue is used to estimate its alignment accuracy. This Neighbourhood is a sphere of radius Srad (in Ångström). A sphere with a 10 Ångström Radius contains between 20-40 amino acids.
Srad
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
1000
T1 - the Distance Threshold
Within a sphere, each pair of aligned residues either agrees or disagrees with the central residues alignment. Pairs of aligned residues whose difference of distance (Delta) is lower than T1 are considered to be supportive, pairs of residues above T1 are considered unsupportive.
T1
0.5
0.6
0.7
0.8
0.9
1.0
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
2.0
2.1
2.2
2.5
T2 - the Neighbourhood Support
The final APDB score indicates the proportion of aligned residues correctly aligned from an APDB point of view. APDB considers that a pair of residues is correctly aligned if T2 percent of its neighbourhood is supportive (as defined above in the T1 section).
T2
20
30
40
50
60
70
80
90
100
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