Difference between revisions of "Task 6 - EVfold"
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For the proteins used in this practical, structures have been determined. However, in real-life projects, you often do not have protein structures only sequences. During this practical, you already predicted secondary structure elements |
For the proteins used in this practical, structures have been determined. However, in real-life projects, you often do not have protein structures only sequences. During this practical, you already predicted secondary structure elements |
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+ | |||
+ | correlated mutations |
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+ | |||
+ | |||
+ | |||
+ | calculating the evolutionary couplings |
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+ | |||
+ | 0. aligment (clustalw.... Pfam alignment good) |
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+ | |||
+ | 1. a2m2lm.... => aligment |
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+ | 2. freecontact -> standard (installed on student computers) |
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+ | |||
+ | Output -> all couplings + evolutionary coupling score (last column) |
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+ | |||
+ | rank by score => look at distrubution, values, range |
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+ | |||
+ | Meaning of score unclear |
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+ | |||
+ | Take only scores for i+6, i.e. neighboring residues neglected, minimal 5 residues between coupled residues |
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+ | |||
+ | Take ranking, check for each coupled pair the actual distance in the structure. TP: distance <= 5 AA (minimal distance of all pairs of all atoms of both residues) |
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+ | |||
+ | |||
+ | EVcoupling |
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+ | Check evolutionary hot spots, i.e. relevant residues, functionally important sites. |
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+ | Take L couplings (L=length of protein sequence), sum scores for each residue. Analyze. |
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+ | (Cell paper) |
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+ | |||
+ | - compare to conservation, single site conservation |
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+ | |||
+ | |||
+ | EVfold.org |
Revision as of 13:43, 4 June 2013
For the proteins used in this practical, structures have been determined. However, in real-life projects, you often do not have protein structures only sequences. During this practical, you already predicted secondary structure elements
correlated mutations
calculating the evolutionary couplings
0. aligment (clustalw.... Pfam alignment good)
1. a2m2lm.... => aligment 2. freecontact -> standard (installed on student computers)
Output -> all couplings + evolutionary coupling score (last column)
rank by score => look at distrubution, values, range
Meaning of score unclear
Take only scores for i+6, i.e. neighboring residues neglected, minimal 5 residues between coupled residues
Take ranking, check for each coupled pair the actual distance in the structure. TP: distance <= 5 AA (minimal distance of all pairs of all atoms of both residues)
EVcoupling
Check evolutionary hot spots, i.e. relevant residues, functionally important sites.
Take L couplings (L=length of protein sequence), sum scores for each residue. Analyze.
(Cell paper)
- compare to conservation, single site conservation
EVfold.org