Discovery Studio Visualizer Tutorial: How to Analyse Docking Results and Make 2D Interaction Diagrams

Answer: Discovery Studio Visualizer turns a docking result into a figure in four steps. Open the receptor, insert the docked pose into the same document, select the ligand and click Define Ligand in the Receptor-Ligand Interactions panel, then click Show 2D Diagram. The diagram names every contact, and File then Save As exports it.

You have a pose. AutoDock Vina printed an affinity, the ligand is sitting in the pocket, and the next thing every supervisor, thesis committee and reviewer asks for is the same picture: a flat, labelled diagram showing which residues touch the ligand and how. This walkthrough produces that figure, and it also covers the part most tutorials skip, which is checking that the interactions in the picture are real before you put your name on it.

Before you start: is Discovery Studio Visualizer the right tool for you?

Two limitations decide this for you, so they belong at the top rather than buried at the end.

It is Windows software. The BIOVIA Discovery Studio 2025 system requirements list Windows and Red Hat or Rocky Linux only. There is no macOS build. If you work on a Mac or a Chromebook, you either run Windows in a virtual machine or you use one of the free alternatives in the comparison table below, which are all browser based or cross platform.

It is free, but you have to register. BIOVIA distributes the Visualizer through a registration form on the Dassault Systemes site, not as a direct download link. Expect to supply an institutional email address. The vendor datasheet is specific about what the free licence includes for structure based work: “Define, display and edit ligand binding sites”, “Create 2D ligand-receptor interaction diagrams”, and “Monitor non-bond interactions including favorable, unfavorable and unsatisfied interactions”. Those three lines are the whole of this tutorial. You do not need a paid licence for any of it.

If you have not run the docking yet, work through our AutoDock Vina tutorial for beginners first, and the molecular docking guide for the method as a whole.

What files do you need, and how do you convert a PDBQT pose?

Discovery Studio Visualizer reads PDB, MOL2 and SD files. It does not read AutoDock’s PDBQT format, which is what Vina writes. You convert first.

Vina’s output file holds every pose it kept, stacked as separate models in one file. Open Babel splits and converts it in one command:

• obabel out.pdbqt -O pose.pdb -m writes every pose to its own file (pose1.pdb, pose2.pdb and so on). The -m option is what performs the split.
• obabel out.pdbqt -O pose1.pdb -f 1 -l 1 writes only the top-ranked pose, using -f for the first entry and -l for the last.

For the receptor, use the same coordinates you docked against. If you prepared the receptor in AutoDockTools and saved it as receptor.pdbqt, either convert that back with obabel receptor.pdbqt -O receptor.pdb or reuse the cleaned PDB you made it from. What you must not do is download a fresh copy from the PDB and load that instead, because any translation applied during preparation will leave your ligand floating outside the pocket. Our guide on preparing a protein and ligand for docking covers where those coordinate changes come from.

How do you load the receptor and the docked pose into one document?

The interaction tools only work when the protein and the ligand are in the same open document. Two routes get you there.

1. Insert route. Open the receptor with File, then Open. With that window active, use File, then Insert From, and choose your converted pose file. The ligand is merged into the open document at its own coordinates.
2. Concatenate route. Build a complex outside the program by appending the ligand’s ATOM and HETATM records to the receptor PDB before the END line, then open the single file. On Linux or macOS: grep -h '^ATOM\|^HETATM' receptor.pdb pose1.pdb > complex.pdb. This is the more reliable route when the insert step misplaces the ligand.

Check the Hierarchy panel after loading. You should see the protein chains and a separate entry for the ligand. If the ligand appears merged into a protein chain, the interaction detection will treat it as part of the receptor and find nothing.

How do you define the ligand so Discovery Studio can find the interactions?

This is the step that stops most people, because nothing happens automatically. Discovery Studio does not guess which molecule is the ligand.

1. Open the Tools panel from the View menu and choose Receptor-Ligand Interactions.
2. Click your ligand in the 3D view, or select it in the Hierarchy panel. The whole molecule must be selected, not one atom.
3. Click Define Ligand. The ligand now carries the LIGAND label, and the rest of the panel becomes active.

You can also define the binding site at this point if you want a surface or a pocket rendering, but the 2D diagram does not require it. Defining the ligand alone is enough.

How do you list every interaction with its distance and type?

With the ligand defined, Show Interactions draws the non-bond contacts in 3D as coloured dashed lines, and Show Distances prints the length of each one in angstroms next to it. The same contacts appear as rows in the Data Table view, which is the part you want, because a table copies into a manuscript and a screenshot does not.

Each row gives you the interacting residue, the interaction category and the distance. Read the categories against the legend the program generates rather than memorising colours, since the palette changes between releases. The datasheet’s three-way split is the one that matters scientifically: favorable contacts are the ones you report, unfavorable contacts are steric clashes or donor-donor repulsions that mean your pose is strained, and unsatisfied flags a buried polar group with no partner. A pose carrying unfavorable bumps is a result you investigate, not a result you publish.

For what those interactions mean for your binding hypothesis, see how to interpret molecular docking results.

How do you generate the 2D interaction diagram?

Click Show 2D Diagram in the same Receptor-Ligand Interactions panel. A new tab opens with the flat schematic: your ligand drawn as a 2D structure in the centre, contacting residues arranged around it as labelled circles, dashed lines for the directional interactions, and shaded arcs for the hydrophobic and van der Waals envelope. A legend is generated with it.

Three edits are worth making before you export.

• Drag the residue labels apart. The automatic layout overlaps labels on a crowded pocket. Every element in the diagram tab can be moved with the mouse.
• Delete the residues you are not discussing. A diagram showing twenty contacts communicates less than one showing the six you mention in the text. Select and delete the rest.
• Turn off van der Waals shading if the figure is about hydrogen bonds. The arcs dominate the image visually and they are the least specific information in it.

How do you export the diagram at a resolution a journal will accept?

Use File, then Save As, and pick an image format. PNG or TIFF, never JPEG, because JPEG compression puts halos around thin black lines and text. Set a transparent background if you plan to place the diagram on a coloured panel in a multi-part figure.

The pixel width you need is set by the journal, not by your screen. Elsevier’s artwork sizing specification requires 300 dpi for halftone images, 500 dpi for combination art and 1000 dpi for line art, at fixed printed widths of 90 mm for a single column, 140 mm for 1.5 column and 190 mm for double column. A 2D interaction diagram is combination art, since it mixes line drawing with shaded arcs, so 500 dpi is your target.

For a single-column interaction diagram, export at 1772 pixels wide or more. Exporting at your monitor’s resolution, which is what happens if you accept the default, gives you roughly 800 to 1200 pixels and a figure the production team will send back.

How do you know the interactions are real and not a display setting?

Every interaction viewer applies distance and angle cutoffs, and different programs use different ones. The same pose can show nine hydrogen bonds in one tool and six in another without either being wrong. This is the single most common reason a reviewer questions an interaction figure.

The defensible move is to profile the pose in a second program and report contacts both agree on. The Protein-Ligand Interaction Profiler (PLIP), published by Adasme and co-workers in Nucleic Acids Research in 2021 (volume 49, pages W530 to W534), is the usual choice because it is free, it runs in a browser on any operating system, and its cutoffs are published in the source code rather than hidden in a dialog. The paper describes the tool as offering “more flexibility by adjustable thresholds, mode and model selection”. Its defaults are worth knowing, because they tell you what a strict definition of each interaction looks like:

Upload the same complex PDB to PLIP, then compare its list against your Discovery Studio table. Contacts that appear in both are safe to build an argument on. Contacts that appear in only one belong in the supplementary material with the cutoff stated, or nowhere.

What are the free alternatives to Discovery Studio Visualizer?

Discovery Studio is not the only route to a 2D diagram, and it is the wrong route if you are not on Windows or if you need to process fifty poses in a loop.

LigPlot+, described by Laskowski and Swindells in the Journal of Chemical Information and Modeling in 2011 (volume 51, pages 2778 to 2786), is the tool behind the diagram style you have seen in structural papers since the 1990s, and its ability to overlay the same binding site from several PDB entries is something Discovery Studio does not do. Most groups end up using two of these rather than one.

Troubleshooting: real errors and their fixes

• Define Ligand is greyed out. Nothing is selected, or your selection is a single atom. Click the ligand in the Hierarchy panel so the entire molecule highlights, then try again.
• The ligand loads far outside the protein. Your receptor file is not the one you docked against. Convert the receptor PDBQT you used in the Vina run back to PDB and reload.
• Show 2D Diagram produces an empty or near-empty picture. The ligand was defined but no contacts were found, which almost always means the two molecules are in different coordinate frames. Measure the distance from a ligand atom to the nearest protein atom. If it is above about 10 A, the frames do not match.
• Discovery Studio refuses to open your file. You handed it a PDBQT. Convert with Open Babel first.
• Hydrogen bonds are missing from an otherwise correct pose. Your structure has no hydrogens. Vina strips non-polar hydrogens and PDB files from the RCSB usually have none at all. Add them before profiling, and state in your methods which program added them.
• The exported image looks blurred at print size. You exported at screen resolution. Set the pixel width explicitly using the table above.

Frequently asked questions

Can Discovery Studio Visualizer open AutoDock Vina output directly?

No. Vina writes PDBQT, which the Visualizer does not read. Convert with obabel out.pdbqt -O pose.pdb -m and open the resulting PDB.

Is Discovery Studio Visualizer really free for a student thesis?

Yes. The visualization and analysis features used in this tutorial, including the 2D interaction diagram, are listed in the BIOVIA datasheet as available without a licence. The paid product adds simulation protocols, not viewing.

Does Discovery Studio Visualizer run on a Mac?

No. The Discovery Studio 2025 system requirements list Windows and Red Hat or Rocky Linux, with no macOS entry. Mac users should run PLIP in a browser or use LigPlot+, which is a Java application.

Which distance counts as a hydrogen bond in a docking figure?

There is no single answer, which is why you state the cutoff. PLIP uses a maximum donor to acceptor distance of 4.1 A with a donor angle of at least 100 degrees. Report the value your software used in the figure caption or the methods section.

What resolution should I export the 2D diagram at?

Treat it as combination art and target 500 dpi at the printed width. For a 90 mm single-column figure that is 1772 pixels wide, following Elsevier’s artwork sizing specification. Save as PNG or TIFF, not JPEG.

Do I need to define the binding site as well as the ligand?

Not for the 2D diagram. Defining the ligand is sufficient. Define the site only when you want a pocket surface or a cavity rendering in the 3D view.

Where this fits in the larger skill set, and what to learn next, is laid out in our computational biology skills roadmap.

Written by the StemSkills Lab team, whose members have more than ten years of combined work in sequence and structural bioinformatics, drug discovery and design, and multiscale molecular modeling.