PatternQuery:Atlas - Revision history

Lukas: /* Protein */

2015-08-05T15:26:49Z

Protein

← Older revision		Revision as of 15:26, 5 August 2015
Line 44:		Line 44:

	==Rubredoxin binding site==		==Rubredoxin binding site==
	[[Image:PatternQuery-Rubredoxin.png\|200px\|thumb\|~~left~~\|Example from ''1b13'' protein.]]		[[Image:PatternQuery-Rubredoxin.png\|200px\|thumb\|right\|Example from ''1b13'' protein.]]

	===PQ expression===		===PQ expression===

Lukas: /* Protein */

2015-08-05T15:25:59Z

Protein

← Older revision		Revision as of 15:25, 5 August 2015
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	The classical C<sub>2</sub>H<sub>2</sub> zinc finger domain is composed of a simple ββα fold, which is stabilized by a zinc ion coordinated by two histidine and two cysteine residues. The fold is often described by the pattern of X<sub>2</sub>-C-X<sub>2-4</sub>-C-X<sub>12</sub>-H-X<sub>3-5</sub>-H, where X stands for any amino acid, C is cysteine and H is histidine.		The classical C<sub>2</sub>H<sub>2</sub> zinc finger domain is composed of a simple ββα fold, which is stabilized by a zinc ion coordinated by two histidine and two cysteine residues. The fold is often described by the pattern of X<sub>2</sub>-C-X<sub>2-4</sub>-C-X<sub>12</sub>-H-X<sub>3-5</sub>-H, where X stands for any amino acid, C is cysteine and H is histidine.


			==Rubredoxin binding site==
			[[Image:PatternQuery-Rubredoxin.png\|200px\|thumb\|left\|Example from ''1b13'' protein.]]

			===PQ expression===
			<syntaxhighlight lang="python">
			Atoms("Fe").AmbientResidues(2.5).Filter(lambda l: l.Count(Residues("Cys")) == 4)
			</syntaxhighlight>

			<br style="clear:both" />

			Rubredoxin active site contains an iron ion which is coordinated by the sulfurs of four conserved cysteine residues forming an almost regular tetrahedron. PQ expression identifies Fe atom coordinated by 4 cysteins.

Lukas at 10:11, 28 July 2015

2015-07-28T10:11:34Z

← Older revision		Revision as of 10:11, 28 July 2015
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	~~__NOTOC__~~		{{TOC limit\|2}}
			=DNA=
	=RNA kink-turn motif (Kt-7)=		=RNA=
			==RNA kink-turn motif (Kt-7)==
	[[Image:PatternQuery-Atlas-Kt-7.png\|200px\|thumb\|left\|Example from ''1ffk'' protein.]]		[[Image:PatternQuery-Atlas-Kt-7.png\|200px\|thumb\|left\|Example from ''1ffk'' protein.]]

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			=Protein=
	=~~C2H2~~ Zinc finger=		==C<sub>2</sub>H<sub>2</sub> Zinc finger==

	[[Image:PatternQuery-Atlas-C2H2.png\|200px\|thumb\|left\|Example from ''4r2a'' protein.]]		[[Image:PatternQuery-Atlas-C2H2.png\|200px\|thumb\|left\|Example from ''4r2a'' protein.]]
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	<br style="clear:both" />		<br style="clear:both" />

	<~~code~~>		The classical C<sub>2</sub>H<sub>2</sub> zinc finger domain is composed of a simple ββα fold, which is stabilized by a zinc ion coordinated by two histidine and two cysteine residues. The fold is often described by the pattern of X<sub>2</sub>-C-X<sub>2-4</sub>-C-X<sub>12</sub>-H-X<sub>3-5</sub>-H, where X stands for any amino acid, C is cysteine and H is histidine.
	~~Some description goes here~~
	</~~code~~>


	=PA-IIL lectin ~~inding~~ site=		==PA-IIL lectin binding site==
	[[Image:PatternQuery-Intro1.png\|200px\|thumb\|left\|Example from ''1gzt'' protein.]]		[[Image:PatternQuery-Intro1.png\|200px\|thumb\|left\|Example from ''1gzt'' protein.]]

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	<br style="clear:both" />		<br style="clear:both" />

	~~<code>~~
	~~Some description goes here~~		The PQ expression searches for 2 calcium ions at most 4Å apart, and all the residues with direct interaction with either of these ions. Furthermore, just the molecular patterns containing a residue with a furan or pyran ring were preserved. Additionally, nucleotides are filtered out as well.
	~~</code>~~

Lukas: Initial fill

2015-07-27T16:08:33Z

Initial fill

New page

__NOTOC__

=RNA kink-turn motif (Kt-7)=
[[Image:PatternQuery-Atlas-Kt-7.png|200px|thumb|left|Example from ''1ffk'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
Near(4,
RegularMotifs(’GGCGAAGAAC’, Type=’Nucleotide’),
RegularMotifs(’GGGAGCC’, Type=’Nucleotide’))
</syntaxhighlight>

<br style="clear:both" />

<code>
Some description goes here
</code>

<br style="clear:both" />

=C2H2 Zinc finger=

[[Image:PatternQuery-Atlas-C2H2.png|200px|thumb|left|Example from ''4r2a'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
RegularMotifs('.{2}C.{2,4}C.{12}H.{3,5}H').
ConnectedAtoms(1).
Filter(lambda m:
m.Find(Atoms('Zn').
ConnectedResidues(1).
Filter(lambda n:
(n.Count(Residues('Cys')) == 2) & (n.Count(Residues('His')) == 2))).
SeqCount() > 0)
</syntaxhighlight>

<br style="clear:both" />

<code>
Some description goes here
</code>

=PA-IIL lectin inding site=
[[Image:PatternQuery-Intro1.png|200px|thumb|left|Example from ''1gzt'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">

Near(4, Atoms("Ca"), Atoms("Ca"))
.ConnectedResidues(1)
.Filter(lambda l:
l.Count(Or(Rings(5 * ["C"] + ["O"]), Rings(4 * ["C"] + ["O"]))) > 0)
.Filter(lambda l: l.Count(Atoms("P")) == 0)
</syntaxhighlight>

<br style="clear:both" />

<code>
Some description goes here
</code>