Sandbox6 Eric Martz - Revision history

Eric Martz: /* Homology Model for 2-88 */

Eric Martz — Wed, 09 Feb 2011 20:47:04 GMT

Homology Model for 2-88

←Older revision		Revision as of 20:47, 9 February 2011
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	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.		* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
-	*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)	+	*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest<ref>ConSurf run with E value cutoff rat default 0.001, Uniref-90 database, 2 PSI-BLAST iterations, 18 sequences after filtration (35%/95%), average pairwise distance in the multiple sequence alignment 1.09, 57 yellow residues. Number of yellow residues was not reduced in a separate run with the E value raised to 0.03, Uniprot database, 3 PSI-BLAST iterations, and filtration at 25%/98%. This gave 22 sequences, APD 0.90, but 65 yellow residues.</ref> (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/2'>Cartoon</scene><table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table>		**<scene name='Sandbox6_Eric_Martz/2-88_conservation/2'>Cartoon</scene><table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table>
-	**Cartoon decorated with conserved residues	+	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/3'>Cartoon decorated with conserved residues</scene>
	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene>		**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene>
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

Eric Martz: /* Homology Model for 2-88 */

Eric Martz — Wed, 09 Feb 2011 20:39:12 GMT

Homology Model for 2-88

←Older revision		Revision as of 20:39, 9 February 2011
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	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
	*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)		*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
-	<table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table>	+	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/2'>Cartoon</scene><table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table>
-	**Cartoon	+
	**Cartoon decorated with conserved residues		**Cartoon decorated with conserved residues
	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene>		**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene>

Eric Martz: /* Homology Model for 2-88 */

Eric Martz — Wed, 09 Feb 2011 20:35:52 GMT

Homology Model for 2-88

←Older revision		Revision as of 20:35, 9 February 2011
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	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
	*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)		*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
		+	<table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table>
	**Cartoon		**Cartoon
	**Cartoon decorated with conserved residues		**Cartoon decorated with conserved residues

Eric Martz: /* Homology Model for 2-88 */

Eric Martz — Wed, 09 Feb 2011 20:33:33 GMT

Homology Model for 2-88

←Older revision		Revision as of 20:33, 9 February 2011
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	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.		* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
-	*~~I am still working on the analysis~~ of evolutionary conservation in ~~this model~~. (~~I ran into some problem~~ with the ~~ConSurf server~~ and ~~am communicating with~~ the ~~group in Tel-Aviv~~.)	+	*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest. (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
		+	**Cartoon
		+	**Cartoon decorated with conserved residues
		+	**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene>
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />

Eric Martz at 23:45, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 23:45:47 GMT

←Older revision		Revision as of 23:45, 7 February 2011
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	{{Template:ColorKey_Amino2CarboxyRainbow}}		{{Template:ColorKey_Amino2CarboxyRainbow}}
	*<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>.		*<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>.
-	*The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model.	+	*The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain rotamer positions are incorrect in a homology model.
	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
-	*The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>.	+	*The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain rotamer positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>.

Eric Martz at 23:44, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 23:44:50 GMT

←Older revision		Revision as of 23:44, 7 February 2011
Line 21:		Line 21:
	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.		* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
-	*~~Analysis~~ of evolutionary conservation in this model ~~was unsatisfactory because only about 20 sequences appeared to be related~~.	+	*I am still working on the analysis of evolutionary conservation in this model. (I ran into some problem with the ConSurf server and am communicating with the group in Tel-Aviv.)
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />

Eric Martz at 20:20, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 20:20:57 GMT

←Older revision		Revision as of 20:20, 7 February 2011
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	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.		* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>		<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
		+	*Analysis of evolutionary conservation in this model was unsatisfactory because only about 20 sequences appeared to be related.
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />

Eric Martz at 20:17, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 20:17:03 GMT

←Older revision		Revision as of 20:17, 7 February 2011
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	* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.		* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.
	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.		* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
		+	<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center>
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />

Eric Martz at 20:16, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 20:16:11 GMT

←Older revision		Revision as of 20:16, 7 February 2011
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	===Homology Model for 2-88===		===Homology Model for 2-88===
	* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.		* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.
		+	* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges.
	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].		*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />

Eric Martz at 20:12, 7 February 2011

Eric Martz — Mon, 07 Feb 2011 20:12:07 GMT

←Older revision		Revision as of 20:12, 7 February 2011
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	===Homology Model for 2-88===		===Homology Model for 2-88===
	* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.		* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity.
-		+	*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb\|model-2-88]].

	===Notes===		===Notes===
	<references />		<references />