Sandbox UC 25 - Revision history

Ignacio Ibarra Del Río at 21:42, 19 December 2012

Ignacio Ibarra Del Río — Wed, 19 Dec 2012 21:42:32 GMT

←Older revision		Revision as of 21:42, 19 December 2012
Line 63:		Line 63:
	After the mentioned filters, the obtained structures set (n=86) was analyzed in terms of sequence to remove repeated motifs presented locally in more than one structure. A dendrogram showing sequence identity between PDB sequences is shown below (left) One representative structure was selected using resolution, pH (between 6.5 and 7.5) and acceptable temperature ranges as criteria, for each group in which the sequence identity was 100%, giving a final set (n=34).		After the mentioned filters, the obtained structures set (n=86) was analyzed in terms of sequence to remove repeated motifs presented locally in more than one structure. A dendrogram showing sequence identity between PDB sequences is shown below (left) One representative structure was selected using resolution, pH (between 6.5 and 7.5) and acceptable temperature ranges as criteria, for each group in which the sequence identity was 100%, giving a final set (n=34).

-	[[File:Example.png~~\|thumb \|alt=Example alt text \|Example caption~~]]	+	[[File:Example.png]]

	In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.		In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.

Ignacio Ibarra Del Río at 21:11, 19 December 2012

Ignacio Ibarra Del Río — Wed, 19 Dec 2012 21:11:09 GMT

←Older revision		Revision as of 21:11, 19 December 2012
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	='''Structural analysis of free DNA duplexes'''=		='''Structural analysis of free DNA duplexes'''=
-	~~<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==~~	+
	According to the current DNA structural data, free DNA duplexes can adopt certain conformations more likely. Examples are shown checking at the available data in the PDB.		According to the current DNA structural data, free DNA duplexes can adopt certain conformations more likely. Examples are shown checking at the available data in the PDB.

Ignacio Ibarra Del Río at 20:30, 19 December 2012

Ignacio Ibarra Del Río — Wed, 19 Dec 2012 20:30:37 GMT

←Older revision		Revision as of 20:30, 19 December 2012
Line 63:		Line 63:
	After the mentioned filters, the obtained structures set (n=86) was analyzed in terms of sequence to remove repeated motifs presented locally in more than one structure. A dendrogram showing sequence identity between PDB sequences is shown below (left) One representative structure was selected using resolution, pH (between 6.5 and 7.5) and acceptable temperature ranges as criteria, for each group in which the sequence identity was 100%, giving a final set (n=34).		After the mentioned filters, the obtained structures set (n=86) was analyzed in terms of sequence to remove repeated motifs presented locally in more than one structure. A dendrogram showing sequence identity between PDB sequences is shown below (left) One representative structure was selected using resolution, pH (between 6.5 and 7.5) and acceptable temperature ranges as criteria, for each group in which the sequence identity was 100%, giving a final set (n=34).

-	[~~DNA_86~~.png\|~~left~~\|~~500px~~]~~[DNA_34.png\|left\|500px~~]	+	[[File:Example.png\|thumb \|alt=Example alt text \|Example caption]]
-		+

	In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.		In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.

Student at 20:25, 19 December 2012

Student — Wed, 19 Dec 2012 20:25:27 GMT

←Older revision		Revision as of 20:25, 19 December 2012
Line 1:		Line 1:
-	'''~~DNA structural~~ analysis'''	+	='''Structural analysis of free DNA duplexes'''=
	<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==		<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==
	According to the current DNA structural data, free DNA duplexes can adopt certain conformations more likely. Examples are shown checking at the available data in the PDB.		According to the current DNA structural data, free DNA duplexes can adopt certain conformations more likely. Examples are shown checking at the available data in the PDB.

-	Sources	+	== Sources ==
	All extracted PDB structures were downloaded from two sources:		All extracted PDB structures were downloaded from two sources:
-	• Nucleic Acid Database (NDB) FTP server, and are represented with their PDB ID code.	+
-	• Protein Data bank PDB	+	* Nucleic Acid Database (NDB) <ref> PMID 1384741 </ref> FTP server, and are represented with their PDB ID code.
-	NDB X-Ray and NMR structures	+	* Protein Data bank PDB <ref> PMID 10592235 </ref>
		+
		+	== NDB X-Ray and NMR structures ==
	The NDB server gives filter options for downloading structures. Briefly, the applied filters are:		The NDB server gives filter options for downloading structures. Briefly, the applied filters are:
-	• Only DNA structures (proteins, RNA and ligands are discarded)	+
-	• No nucleic acid modifications (base, sugar or phosphate)	+	* Only DNA structures (proteins, RNA and ligands are discarded)
-	• No triplex, quadruple, or single stranded helices*	+	* No nucleic acid modifications (base, sugar or phosphate)
-	• No internal loops, tetraloops, hairpin loops, or bulged bases are allowed.	+	* No triplex, quadruple, or single stranded helices <ref> B-DNA double helices are classified according to the author who uploaded the PDB. </ref>
-	• No 3-4 way junctions.	+	* No internal loops, tetraloops, hairpin loops, or bulged bases are allowed.
		+	* No 3-4 way junctions.
		+
		+	== Protein Data bank PDB ==
		+
		+	All free DNA structures were downloaded from the PDB, and the same filters applied for NDB were used.
		+
		+	== Data collection problems ==
		+
		+	=== Files not found ===
		+
		+	Certain obtained results given by the NDB server did not have associated files. Particularly:
		+
		+	==== X-ray ====
		+
		+	# '''bdj061''' (PDB ID not linked to NDB ID): It gives a reference link to a Nature’s paper http://www.nature.com/nature/journal/v368/n6470/abs/368469a0.html. However, the PDB ID does not exist inside the NDB files. The described structure corresponds to the Trp operon operator site. The paper was not publicly available to get the old PDB ID and checked why it was changed (Discard if reference is not available).
		+
		+	==== NMR ====
		+	# '''2kal''': Found in the NDB but with broken links. Proper files were downloaded from the PDB (PDB ID 2KAL).
		+	# '''2k1y''': idem. (PDB ID 2K1Y).
		+
		+	=== Modified structures ===
		+	Even though the NDB server structures had stated filters for modified nucleic acids, posterior analysis showed modified bases in several files. The reported set was checked and structures were discarded if a modification was found, via manual analysis.
		+
		+	==== NMR (41 modified structures) ====
		+
		+	1k8l, 1k8n, 1laq, 1las, 1mk6, 1mkl, 1oq2, 1s0t, 1s74, 1s75, 1s88, 1sp6, 1tuq, 1u6n, 1uab, 1xci, 2hli, 2hmd, 2hmr, 2hou, 2k1y, 2kal, 2kd9, 2kda, 2kh3, 2kh5, 2kh6, 2kh7, 2l2u, 2l2v, 2l8p, 2lfa, 2lfx, 2lfy, 2lg0, 2lho, 2lib, 2lsc, 2lsz, 2lt0, 2rrq
		+
		+	==== X-ray (9 modified structures) ====
		+
		+	458d, 2qef, 2qeg, 122d, 123d, 3bna, 4bna, 329d, 3n4n
		+
		+	=== More filters ===
		+
		+	# Abasic sites - NMR (4 structures): 2hsk, 2hsl, 2hsr, 2hss
		+	# Nicked structures - X-ray (2 structures): 1ndn, 1vte
		+	# Triangular assimetryc units - X-ray (1 structure): 3nao
		+	# 4 way junction - X-ray (1 structure): 3q5c
		+	# Triple helix - X-ray (1 structure): 272d
		+	# Resolution (Lower than 3.0)
		+	# Redundancy (99% sequence ID)
		+
		+	=== B-DNA dinucleotides filter '''[OBSOLETE AND NOT INCLUDED]'''===
		+	A filter to differentiate between different right-handed DNA dinucleotides was described in the Olson’s group 3DNA paper <ref>PMID 18600227</ref>. The method identifies DNA populations that can be visualized using Zp(h) vs. Zp plots (B-DNA = bottom distribution). With this criterion, 3DNA was applied to classify all dinucleotides available in the current set, and structures with less than half of B-DNA dinucleotides were discarded (Note. This is strongest filter applied)
		+
		+	== Redundancy reduction ==
		+	After the mentioned filters, the obtained structures set (n=86) was analyzed in terms of sequence to remove repeated motifs presented locally in more than one structure. A dendrogram showing sequence identity between PDB sequences is shown below (left) One representative structure was selected using resolution, pH (between 6.5 and 7.5) and acceptable temperature ranges as criteria, for each group in which the sequence identity was 100%, giving a final set (n=34).
		+
		+	[DNA_86.png\|left\|500px][DNA_34.png\|left\|500px]
		+

	In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.		In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.
		+
		+	== References ==
		+
		+	<references/>

Student at 19:21, 19 December 2012

Student — Wed, 19 Dec 2012 19:21:27 GMT

←Older revision		Revision as of 19:21, 19 December 2012
Line 1:		Line 1:
	'''DNA structural analysis'''		'''DNA structural analysis'''
	<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==		<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==
-	According to the current DNA ~~information~~ available in the PDB, ~~certain short sequence patterns adopt a Z~~-~~DNA conformation more likely~~. ~~Examples of~~ structures ~~that~~ are ~~included in this group~~ are	+	According to the current DNA structural data, free DNA duplexes can adopt certain conformations more likely. Examples are shown checking at the available data in the PDB.
		+
		+	Sources
		+	All extracted PDB structures were downloaded from two sources:
		+	• Nucleic Acid Database (NDB) FTP server, and are represented with their PDB ID code.
		+	• Protein Data bank PDB
		+	NDB X-Ray and NMR structures
		+	The NDB server gives filter options for downloading structures. Briefly, the applied filters are:
		+	• Only DNA structures (proteins, RNA and ligands are discarded)
		+	• No nucleic acid modifications (base, sugar or phosphate)
		+	• No triplex, quadruple, or single stranded helices*
		+	• No internal loops, tetraloops, hairpin loops, or bulged bases are allowed.
		+	• No 3-4 way junctions.
		+
		+	In the current project, 34 free DNA structures have been selected via filtering of the entire PDB-DB, using the following criteria.

Student: New page: '''DNA structural analysis''' == Your Heading Here (may...

Student — Wed, 19 Dec 2012 16:13:26 GMT

New page: '''DNA structural analysis''' <Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (may...

New page

'''DNA structural analysis'''
<Structure load='1m6r' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />== Your Heading Here (maybe something like 'Structure') ==
According to the current DNA information available in the PDB, certain short sequence patterns adopt a Z-DNA conformation more likely. Examples of structures that are included in this group are