Difference between revisions of "Lab journal task 4"
From Bioinformatikpedia
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LGA: <br> |
LGA: <br> |
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− | * superimpose to target structure (second structure, |
+ | * superimpose to target structure (second structure, in our case 1A6Z ) |
* default parameters |
* default parameters |
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SSAP: <br> |
SSAP: <br> |
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* no parameters to set |
* no parameters to set |
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*score from 0 to 100 |
*score from 0 to 100 |
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+ | TopMatch: <br> |
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+ | * target 1A6Z |
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+ | * default parameters |
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+ | * target in blue, query in green |
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+ | * structurally equivalent residue pairs: orange (query) and red (target) |
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+ | * S = Measure of structural similarity based on Gaussian functions (see Sippl & Wiederstein (2012)). If the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0. |
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+ | * S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012). |
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+ | Er |
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+ | |||
number of alignet residues per pair |
number of alignet residues per pair |
Revision as of 23:57, 10 August 2013
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The following four alignment methods were used:
- superimpose to target structure (second structure, in our case 1A6Z )
- default parameters
- no target structure to specify
- no parameters to set
- score from 0 to 100
- target 1A6Z
- default parameters
- target in blue, query in green
- structurally equivalent residue pairs: orange (query) and red (target)
- S = Measure of structural similarity based on Gaussian functions (see Sippl & Wiederstein (2012)). If the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0.
- S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012).