Our showcase of PoseEdit’s features is based on the structure of a lysine-specific histone demethylase 1A (LSD1, PDB code: 5LGT) in complex with the inhibitor 4-methyl-N-[2-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide (ProteinsPlus identifier: 6W3_A_902) and an flavin adenine dinucleotide (FAD) cofactor (ProteinsPlus identifier: FAD_A_901) in the same binding site [25]. First, we will demonstrate how users can verify the chemical information content of a diagram. Next, we will show how users can optimize a diagram according to objective layout quality issues. Last, we will exemplify how users can further customize a diagram by editing its chemical information content and graphical restyling.

The affinity of a ligand does not depend on user’s taste. What may depend on user’s taste is the degree of focus to put on the various interactions contributing to ligand affinity. Interaction models are based on different studies and apply various different criteria to decide on the presence or absence of an interaction. The choice of the supported interaction types, their geometric parametrization, and the structure types as interaction partners may not always match the user’s expectations. Depending on the individual thresholds, experienced users might come to different assessments on the presence of specific interactions. Therefore, they might be skeptical that the automatically generated diagram accurately represents the chemical information they would have picked themself, or they might already be aware of discrepancies. This section will show how to explore the inhibitor’s environment beyond the pre-calculated diagram, providing the users with ideas to modify its chemical information content with PoseEdit. Figure 5 shows the PoseEdit diagram of the inhibitor 6W3_A_902 in complex with its target automatically generated by PoseView. The exported diagram in JSON format is available in the Supplementary Information (Online Resource 1).

PoseEdit diagram of lysine-specific histone demethylase 1A in complex with an inhibitor 4-methyl-N-[2-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide (PDB code: 5LGT; ProteinsPlus identifier: 6W3_A_902). The following ligand interactions are depicted in the diagram: an ionic interaction with residue Asp555A, a pi–pi interaction with residue Trp695A, hydrophobic contacts with residues His564A, Phe538A, Ala539A, and Val333A

Users can load and inspect the pose with the ligand-associated 3D binding site from the central Pocket list (ProteinsPlus pocket identifier: FAD_A_901_6W3_A_902) in the 3D viewer. The PoseEdit diagram of the inhibitor is an excerpt from this 3D binding site. While the diagram displays ligand interactions with protein and nucleic acid residues and metals, the 3D binding site also shows all non-interacting structural elements and additional interaction partners that are not included in a PoseEdit diagram by default, such as water molecules. Therefore, the 3D binding site is a suitable starting point for verifying the chemical information content of the diagram resulting in ideas of how to extend it. The 2D-3D synchronization feature supports the user’s exploration of the ligand binding mode in both visualizations. Structural diagram objects in the 2D editor that are selected via the Select mode and consequently highlighted in dark green are automatically focused and highlighted in the 3D viewer as well. In addition, when users place the mouse pointer over any unselected or selected structural diagram object in the 2D editor or 3D viewer, it is highlighted with a light green color in both depictions. A Select mode option dictates how and what is selected. Users can select multiple atoms, bonds of structures, and structure circles via a rectangular and lasso selection tool with the Rectangle and Lasso option. With the Click option, users can pick single atoms, bonds, structure circles, as well as text labels.

Users can, for instance, select the atoms and bonds of all structures and the three text labels of the hydrophobic residues His564A, Phe538A, and Ala539A to highlight the corresponding structures in the 3D viewer. This feature enables an easier comprehension of already covered aspects of the 3D binding site and potential additional chemical information to be included. Interesting chemical information in the 3D binding site that is not depicted in the PoseEdit diagram is, for instance, the ligand FAD_A_901, the FAD cofactor. This cofactor interacts not only with the protein binding site via ionic interactions and hydrogen bonds but also with the inhibitor via pi-stacking interactions. Interactions with cofactors other than metal like FAD are not included in a PoseEdit diagram by default but might be relevant. The following section will provide more insights into the ligand binding mode of the cofactor by inspecting its PoseEdit diagram.

Concerning the occurrence of overlaps and intersections of graphical objects, especially those diagrams that condense a large amount of chemical information closely arranged in 3D space may need to be manually revised. A highly complex interaction pattern makes it algorithmically more challenging to depict a diagram in 2D, which may result in a lower layout quality. The diagram of the FAD cofactor mentioned previously is an example of such an objectively suboptimal layout caused, for example, by the adjacent and non-planar diphosphate group undergoing numerous hydrogen bond and ionic interactions. Such functional groups often contribute to crowded diagrams. Figure 6 shows the cofactor’s unmodified PoseEdit diagram. Figure 7 shows the diagram after manual optimization of the layout. The corresponding JSON files can be accessed in the Supplementary Information (Online Resource 2 and 3). A screen recording video that illustrates the following textually described diagram optimization procedure is given in Online Resource 4.

PoseEdit diagram of lysine-specific histone demethylase 1A in complex with a cofactor (PDB code: 5LGT; ProteinsPlus identifier: FAD_A_901) with a suboptimal layout

PoseEdit diagram of lysine-specific histone demethylase 1A in complex with a cofactor (PDB code: 5LGT; ProteinsPlus identifier: FAD_A_901) with a layout optimized by PoseEdit

As the necessary modifications for optimizing a diagram may not be immediately visible, users might have to experiment with the editor’s functionality. The editor’s history, which is accessible via the Undo and Redo buttons enables, for instance, a trial-and-error approach. In addition, the possibility of hiding structures in the diagram via the editor’s top structure list helps to focus on a specific aesthetic issue and, consequently, quickly find ways to solve it.

The first aesthetic problem to fix is the curved ligand structure. This representation could be more appealing. In addition, the bent ligand structure surrounds and squashes the residues Glu308A, Val811A, and Ser289A such that the two hydrogen bonds of Glu308A cross the structure of Ser289A. The ligand structure can be elongated with the Mirror mode and the Bond option. By left-clicking on a bond, users can cycle through all possible mirroring positions until the most appropriate one is found. In this case, the Mirror mode is applied once on both phosphate anhydride bonds. Thereby, the diphosphate group is unchanged, and the non-bridging oxygen atoms that interact with Arg316A are still on the same side of the ligand, which prevents the crossing of Arg316A intersections with the ligand structure. Using the Rotation mode, the ligand is then rotated counterclockwise into a horizontal position. Subsequently, intersection- and overlap-free positions can now be found for all residues except Arg316A with the Move mode and Rotation mode. A structure’s mirroring, rotation, or movement also affects all associated interactions, hydrophobic contact splines, and text labels, simplifying such structural modifications. Further layout optimization can be achieved by reorienting the hydrogen atoms of the ligand towards the acceptor oxygen atoms of Glu308A by mirroring their bonds with the Mirror mode and by repositioning overlapping text labels of the hydrophobic contacts with the Move mode, which also creates more space for a better placement of Arg316A and Glu308A.

Next, we address the issue that the ligand’s diphosphate group engages in several intersecting hydrophilic interactions with Arg316A. No intersection-free position can be found for that residue by rotation and translation alone. By once mirroring the CB–CG bond of Arg316A with the Mirror mode, Arg316A can be moved and rotated such that its structure is not intersected anymore by the hydrogen bond that originates from its backbone. However, that hydrogen bond still intersects several interactions of the Arg316A side chain, which interact with a second non-bridging oxygen atom of the diphosphate group. Since the two non-bridging oxygen atoms are chemically equivalent in the diagram, users can avoid these intersections in two ways. Either users can remove the interactions of both non-bridging oxygen atoms with the Remove mode and add them with the Add mode to the equivalent one, or users can flip the positions of the two non-bridging oxygen atoms with the Move mode. The diagram is now free of overlaps and intersections and can be exported as a JSON file.

This section will exemplify how to obtain a personalized diagram in terms of information content and graphical styles based on the diagram of the inhibitor and the optimized one of the FAD cofactor. Figure 8 shows an example of an individually customized diagram. The exported JSON file of the diagram is deposited in the Supplementary Information (Online Resource 5).

PoseEdit diagram obtained by the merging of the two diagrams of the LSD1 inhibitors with the ProteinsPlus identifier 6W3_A_902 and FAD and subsequential chemical editing and graphical restyling

Users might, for instance, prefer a single, comprehensive diagram that includes the inhibitor, the cofactor, the interactions between the ligands, and their interactions with the protein binding site rather than two distinct diagrams. The information of the two diagrams can be combined by two approaches. The first one is to individually add the structures, interactions, hydrophobic contact splines, and text labels displayed in one diagram to another one with the Add mode. Structures can be specified by SMILES strings or via a list containing a preselection of frequently appearing binding site structures, from which users can select, for example, the interacting residues. Ligands like the inhibitor or FAD cofactor are not in the list and must be added via the corresponding SMILES strings, which can be obtained from the central Ligand list. Subsequently, the Add mode can be used to draw all missing interactions, hydrophobic contact splines, and text labels. The second and more straightforward and efficient approach is the merging of the two diagrams with the JSON import feature of PoseEdit. Users can, for example, export the JSON file of the diagram of the inhibitor and import it into the optimized diagram of FAD via the button with the JSON text label and plus sign. The imported diagram is automatically placed next to the one of FAD. Multiple structures can be selected and subsequently moved and rotated, along with all linked interactions, hydrophobic contact splines, and text labels using the Select mode’s rectangle or lasso selection tool. Based on the 3D binding site information, users can select all structures of the diagram of the inhibitor and apply the Move mode and Rotation mode such that the two interacting aromatic ring systems of both ligands are adjacently placed. The missing pi-stacking interactions between the ring systems can then be drawn with the Add mode.

Based on the merged diagram, another subjective adjustment exemplified here regards the Nε nitrogen atom of the Arg 316A side chain. This atom is involved in a hydrogen bond as well as an ionic interaction with the same ligand atom. Users might want to keep only the stronger intermolecular force, the ionic interaction. With the Remove mode, users can remove the nitrogen atom’s hydrogen bond and its explicitly drawn hydrogen atom. The nitrogen atom can then be annotated with one implicit hydrogen atom using the Edit mode.

Since the diagram is very complex, users might consider also reducing the diagram’s complexity to avoid overloading the viewer with information or to focus on specific aspects like the atomic interactions with the protein residues. In this regard, the Edit mode can be useful, for example by changing the representation style of Trp695A, which is involved in a pi-stacking interaction, to the Circle representation.

Finally, users can modify all graphical styles in the diagram via a comprehensive configuration list to further individualize the diagram. The list is accessible via the Opts button and contains numerous styling options for atoms, bonds, interactions, structures, structure circles, the editor’s control elements and the diagram background. Users can freely experiment with custom settings since the editor’s editing history tracks all changes. PoseEdit also offers a list of several preset themes. To exemplify the various styling possibilities, the Dark theme, which might be an eye strain-reducing alternative for some users, was used to recolor the background and structures in the diagram. The customized and final diagram now contains the user-desired chemical information and graphical styles.