My software notes

May 16, 2011

statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)

Filed under: web — kpwu @ 4:48 pm
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Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011.

Molecules with sequence length longer than 1200 residues are also excluded. There are 5075 and 2 structures determined by X-ray and NMR methods, respectively in this category.

FYI: I obtained individual numbers from this statistics page at PDB.

Sequence length-dependent distribution plots of X-ray and NMR-determined protein structures.

The magnified NMR section.

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May 9, 2011

Examples of Ramachandran plots of residues in helix, strand or coil regions

Filed under: softwares and scripts — kpwu @ 4:56 pm
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Few weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played around and try to use GnuPlot 4.4 to make my own Ramachandran plots.

Here are three examples of the residual Ramachandran space regarding to the helical, extend or coil regions. I used STRIDE to define the secondary structural regions and obtain the phi/psi angles.

It is quite convenient to plot my own Ramachandran plots in different purposes using this defined plot. I can now have my customized style. ie. I can have different (background) colors, size of dots and high-resolution output image files.

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