Task 5: Homology Modeling

lab journal task 5

1A6Z chain A was used as modeling target in all three methods.

Modeller

We used Modeller to create models based on a single template and multiple templates.

Single template

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<figtable id="Modeller single">

Table 1:Template structures and their sequence identity to the target, as computed by Blast. The RMSD and TM score are given as a quality measure for the different models based on a pairwise sequence alignment with dynamic programming (std Alignment), pairwise sequence alignment with additional secondary structure information (2d Alignment) and manually curated alignments (curated Alignment).

Template	Seq. identity	std Alignment		2d alignment		curated Alignment
		TM score	RMSD	TM score	RMSD	TM score	RMSD
1QVO_A	39%	0.6241	3.647	0.5653	4.994
1S7X_A	29%	0.3355	15.806	0.2509	18.099
1cd1_A	21%	0.3640	18.066	0.4697	5.640

</figtable>

<xr id="Modeller single"/> lists the selected templates and the Modeller results for the different template structures and alignment methods. In addition to the standard pairwise sequence alignment based on dynamic programming, we also used Modeller's alignment.alig2dn() method to improve the alignment by including secondary structure information and improved the alignments manually.

MSA:

"close" homology
1rjz_D	0.34
1zag_A	0.36
1QVO_A	0.39

distant homology:
3huj_C	0.23
1cd1_A	0.21
1VZY_A	0.14

MIX:

1cd1_A 0.21

1QVO_A 0.39