Protein structure prediction from evolutionary sequence variation (Phenylketonuria)
Contents
Summary
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Multiple Sequence Alignment
Lab journal
The multiple alignment of Ras (PF00071) was downloaded from Pfam.
For our protein two domains are included (ACT and Biopterin domain).
Results
Freecontact
is a program that takes a multiple alignment and can calculate the mutual information score and the corrected norm contact score.
- MI:...
- CN:...
H-Ras
Lab journal
<figtable id="cn-ras">
Ten results with highest CN for all and for extracted pairs | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The ten results of freecontact
calculated for H-RAS with highest CN-value first for all pairs and second only for pairs with a distance of at least five residues. Both tables show the position of the first residue in column one with its corresponding amino acid (column 2) and of the second residue in column three with its amino acid in column four. The next one represents the mutual information score (MI) and the last one the corrected norm contact score(CN).
</figtable>
<figure id="cn_distr_ras">
</figure>
Comparing the best ten CN-scores for all and for residue pairs with at least a distant of more than five amino acids it is remarkable that for all pairs the ten best all are directly neighboring amino acids and have almost twice of the CN-score. The range of the CN-score goes from -0.65 to 3.40 for the extracted residue pairs. The distribution can be viewed in <xr id="cn_distr_ras"/>. Additionally the distribution of all residue pairs is shown. They are very similar, nevertheless the range of all pairs goes up to 6.01.
PH4H_HUMAN
<figtable id="cn-pah">
Ten results with highest CN for all and for extracted pairs | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The ten results of freecontact
calculated for the biopterin domain of PAH with highest CN-value first for all pairs and second only for pairs with a distance of at least five residues. Both tables show the position of the first residue in column one with its corresponding amino acid (column 2) and of the second residue in column three with its amino acid in column four. The next one represents the mutual information score (MI) and the last one the corrected norm contact score(CN).
</figtable>
Distribution of CN-Scores: <figure id="cn_distr_ras">
</figure>
Discussion
Calculate structural model
Lab journal
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References
<references/>