Data set summary
This section presents a summary of the set of ligands previously chosen, with some statistics about them, as the number and types of atoms, the types of interactions, among others.
All data
This subsection provides a table with all ligands with the following columns: PDB id, Chain, Ligand, Ligand Number (Residue sequence number), Cluster, # Atoms (Ligand), # Protein-ligand interactions.
The column Cluster refers to the the group to which the ligand was associated using Chemaxon software to perform ligand clustering.
View details on ligand atoms: by clicking on this check button, users can see the number of each type of atom Acceptor, Aromatic, Donor, Hydrophobic, Negative, Positive and even those which do not have a type associated, which we call Unrated.
View details on protein-ligand interactions: by clicking on this check button, users can see the number of each type of interaction Aromatic stacking, Hydrogen bond, Hydrogen bond (water), Hydrophobic, Repulsive and Attractive.
Download data set summary: by clicking on this this button, users can download the table as a .CSV file.
Search: users can type a word to search for in the table.
There are two icons in PDB id column:
Graph: by clicking on this icon a panel will pop up in the screen. In this panel, we provide an interactive view of the Protein-ligand interactions in 3D and 2D (graph). It is available to users the following set of features:
Show/Hide cartoon: protein is displayed in cartoon mode.
Show/Hide surface: protein surface is shown.
Show/Hide residue labels: provides labels with the name of residues which interact with a ligand.
Show/Hide atom labels: atom labels from residues which interact with a ligand are displayed.
Also, there are Residue name and Residue Number text boxes, where users can select and color residues in the Protein visualization by their name or number. The buttons Search and Clear show the selected residues and clear the selection respectively.
Show/Hide atoms by their types: there are six types of atoms which can be displayed simultaneously or not: Acceptor, Aromatic, Donor, Hydrophobic, Negative and Positive.
Show/Hide interactions: there are five types of interaction which can be displayed simultaneously or not: Aromatic stacking, Hydrogen bond, Hydrogen bond (water), Hydrophobic, Repulsive and Attractive.
Show/Hide interacting residues: all interacting residues are provided and users can choose among them which should be displayed.
Reset graph: selects all the atoms (nodes) and its interactions on the Graph. Consequently, all interactions will be displayed in the Protein visualization.
Protein screenshot and Graph screenshot: users can save an image from the Protein or Graph visualization.
Mouse interactions: users can filter interactions in the Protein view by clicking over the nodes in the Graph visualization. A double click with the Mouse left button, selects one atom and its interactions and remove all the other selections. On the other hand, if the user press Ctrl and click with the Mouse left button over a node, it will remove/add an atom and its interactions to the current selection.
Node size (%): increase/reduce the size of the graph nodes to fit well in the panel.
Show/Hide nodes label: provides labels to the graph nodes.
World: by clicking on this icon, users are redirected to protein entry (PDB id) from the specific row directly from PDB website.
By clusters
The set of ligands were clustered according to their physicochemical properties using Chemaxon software. In this subsection, users can see the ligands separated by clusters.
Also, users can search for a PDB entry of interest to check the cluster to which this entry was associated using Search text box.
To see details of all the other features, please refer to All data subsection.