Sandbox UC 25
From Proteopedia
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'''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 | + | 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. | ||
Revision as of 19:21, 19 December 2012
DNA structural analysis
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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.
