ValTrendsDB

Examples

This page offers selected examples that let users discover the full potential in terms of presentation prowess that the ValTrendsDB database has.

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Visualizing quality and features of user's PDB entries

The ValTrendsDB database offers plots of trends between pairs of various factors (for details, please consult the Help that contains a more roundabout introduction to this functionality). These plots are not static though: You can add your own data points to them. That way, you can compare features and/or quality of a PDB entry to the trend of a plot of two factors. The only thing you need to know is the PDB ID of the structures which values you want to compare to the trend. The values are visualized in the plot as green dots. You can hover over the dots to see their ID as well as their values on the X-axis and Y-axis.

Main views of user's PDB entries, which ValTrendsDB offers, are:

Single structure view: Quality of the 1tqn entry

On the two figures below, you can see the trends in plots of two relationships: A relationship of clashscore structure quality factor in regard to the year of release, and a relationship of percentage of Ramachandran outliers structure quality factor in regard to the resolution of a structure model. Values of a structure of human microsomal cytochrome P450 3A4 that qoes by the PDB ID of 1tqn are visualized in both plots by a green point. This way you can see that the PDB structure 1tqn has lower quality than other structures published in the same year, or with the same resolution.

Note: Here are links that will lead you to page Explore relationships that is set up to produce the exact same plot as you see here among the examples: Plot 1, Plot 2.



Protein family structures view: Quality of protein structures of the cytochrome P450-cam family

The plot below shows the relationship of the Ramachandran outliers structure quality factor and the year of release factor. Values of 124 PDB structures of the cytochrome P450-cam family are visualized using green points on top of the trend that is already present in the plot of the relationship. You can see that this protein family contains one structure with markedly lower quality (represented by high value of the clashscore): it is the PDB structure 2h7s.

Note: Here is the link that will lead you to page Explore relationships that is set up to produce the exact same plot as you see here among the examples.



Author's structures view: Structures deposited by Dr. Josef Houser

The plot below shows a relationship between clashscore structure quality factor and structure resolution factor. Values of 13 PDB entries that have been deposited to the PDB database by Dr. Josef Houser are visualized in the plot by green points. The plot demonstrates that structures deposited by Dr. Houser have markedly better quality than average.

Note: Here is the link that will lead you to page Explore relationships that is set up to produce the exact same plot as you see here among the examples.



Journal structures view: A comparison of quality of structures published in journals Nature and Structure

The two plots below depict a relationship of the Ramachandran outliers structure quality factor and the year of release factor. On the top of this trend, we show quality of structures published in journals Structure and Nature. The first plot (Structure journal) contains an additional trend in green that is built from 5 170 PDB entries, while the second plot (Nature journal) has one built from 3 133 PDB entries. Since there were a lot of data points per each journal, both plots visualize only their average values (green points) and medians (short green lines). We can see that Nature structures have markedly lower quality, which is probably caused by journal’s strong pressure on innovativeness and cutting edge approaches.



Note: Unfortunately, these plots cannot be realized as the interactive embedded ones because of the 2 000-character URL length limit that contemporary internet browsers have. This limit is relevant to you if you want to provide IDs to the webpage via its link (using the address bar of you browser, or embedding a ValTrendsDB plot into your own webpage). You can, however, recreate them by visualizing PDB IDs, which list is linked to each PDB entry count in this paragraph, in this plot on the Explore relationships webpage. Do not forget do enable the Show average and median for PDB IDs option as well.