Graphical analysis
This section provides visual representations as bar, pie and pareto charts as well as scatter plots to provide statistics about ligand atom types and their interaction with proteins.
Atoms type (all data)
Summarize atom type information for the ligand set. A set of 8 buttons are provided, one for each atom type plus View all button.
View all: by clicking on this button users must select Bar charts or Pie charts. This button provides a general view of atom types summary data, where bar or pie charts are exhibited for all atom types.
Sort pie chart by: the pie chart slices can be sorted by # Atoms or by Frequency.
Select slices by frequency: slices can be selected (highlighted) Bottom-up or Top-down according to a threshold (on the size of the slice). Also, the user can clear the selections.
Acceptors, Aromatics, Donors, Hydrophobics, Negatives, Positives, Unrated: these buttons provide bar and pareto charts in the same graph and also a pie chart for their respective atom type.
Bar and pareto chart: X axis represents the number of atoms of a certain type (acceptors in this case) and the left hand side Y axis represents the number of ligands. So, we have Y ligands with X atoms of a certain type (acceptors in this case). The right hand side Y axis shows the cumulative frequency of ligands. So, we have Y% of ligands of a certain type (acceptors in this case) until a specific bar in X axis. Note that Y axis in this case refers to the index of the bar in X axis (first, second, etc) and not to X axis itself.
Pie chart: the size of slices represents the cumulative frequency of ligands, the color represents the number of atoms of a certain type (acceptors in this case). By passing the mouse over the slices, a pop-up provides the # Atoms (number of atoms of a certain type - acceptors in this case), Absolute value (number of ligands) and Frequency (cumulative frequency of ligands). Users can also sort slices in pie chart and select slices as detailed in View all button.
Atoms type (all data)
Summarize atom type information for each cluster of ligands. Note that each cluster refers to the the group to which the ligand was associated using Chemaxon software to perform ligand clustering. A set of 7 buttons are provided, one for each atom type. For each atom type button, users can choose among three types of charts: Show bar chart, Show grouped bar chart, Show pie chart.
Interactions type (all data)
Summarize interaction type information for the ligand set. A set of 7 buttons are provided, one for each interaction type plus View all button.
View all: by clicking on this button users must select Bar charts or Pie charts. This button provides a general view of interaction types summary data, where bar or pie charts are exhibited for all interaction types.
Aromatic stacking, Hydrogen bond, Hydrogen bond (water), Hydrophobic, Repulsive, Attractive: these buttons provide bar and pareto charts in the same graph and also a pie chart for their respective atom type in the same way detailed in Atoms type (all data) subsection.
Interactions type (clusters)
Summarize interaction type information for each cluster of ligands. Note that each cluster refers to the the group to which the ligand was associated using Chemaxon software to perform ligand clustering. A set of 5 buttons are provided, one for each interaction type. For each interaction type button, users can choose among three types of charts: Show bar chart, Show grouped bar chart, Show pie chart.
Atoms x interactions
In this subsection we provide a scatter plot which shows if there is potential correlation between a certain type of atom (in the X axis) and its respective interaction type (in the Y axis). For each ligand, we plot a point whose X axis represents the number of atoms of a certain type and the Y axis represents the number of interactions associated with the type of atom in X axis.
View all: by clicking on this button the user have a panoramic view of all scatter plots, with all types of atoms and interactions.
Acceptors, Aromatics, Donors, Hydrophobics, Negatives, Positives, Unrated: each of these buttons provide a scatter plot which presents the atom type (the same from the button) in X axis and the interaction type in Y axis. Note that positive and negative atom types are related to both repulsive and attractive interaction types, thus in this case the scatter plot has two types of points, one for each interaction type.