User:Eric Martz/Cavities tests: Difference between revisions

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This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.

Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command select temperature >50).

Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command select temperature >50). Three of these regions are explained by gaps in the template model (see below).

The [[Conservation, Evolutionary|evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The [http://consurf.tau.ac.il/results/1222995227/output.html run shown here] used 100 sequences from Uniprot, with an APD of 1.4.</ref>

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[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol]

==Gaps in the Template Model==

The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).

@@ Line 18: / Line 18: @@
 This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.
-Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>).
+Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). Three of these regions are explained by gaps in the template model (see below).
 The [[Conservation, Evolutionary|evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The [http://consurf.tau.ac.il/results/1222995227/output.html run shown here] used 100 sequences from Uniprot, with an APD of 1.4.</ref>
@@ Line 25: / Line 25: @@
 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol]
+==Gaps in the Template Model==
 The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).