Drug Design Studio (DDS 2.0)

An all-in-one desktop platform for network pharmacology, covalent & non-covalent docking and virtual screening

Drug Design Studio brings the entire structure-based design workflow (receptor and ligand preparation, binding-site setup, covalent and non-covalent docking, virtual screening, interaction analysis, visualization and molecular-dynamics export)—together with a complete network-pharmacology module—behind one sleek, easy-to-use interface. Free and cross-platform, with the docking workflow running fully offline.

Download for Windows and macOS

What is DDS?

Molecular docking and virtual screening typically require juggling several separate programs for preparation, docking, analysis and visualisation—a real barrier for students and experimental scientists—and covalent docking is harder still, usually demanding expert, command-line protocols. Drug Design Studio (DDS) removes that barrier. Built around simplicity, it is a single, guided desktop application that integrates trusted open-source engines (AutoDock Vina, RDKit, Meeko, Open Babel and 3Dmol.js), allowing the user to move from a protein structure to a ranked, annotated, publication-ready result—covalent or non-covalent—without ever leaving one window. DDS serves as a convenient one-stop platform for the early stages of a drug-discovery workflow, feeding cleanly into downstream molecular-dynamics studies. Beyond structure-based design, DDS also includes a complete network-pharmacology module—mapping compounds and diseases to their shared targets, protein–protein interaction networks, hub genes and enriched GO/KEGG pathways—and links those hub genes directly back into the docking and virtual-screening workflow, so systems-level and structure-based analyses live in the very same application.

Key features

All-in-one workflow
Receptor, ligand, binding site, docking, analysis and export, all in one guided interface.

Covalent & non-covalent docking
Standard docking plus a built-in covalent mode: automatic warhead detection, interactive reactive-residue targeting, and two protocols—fast geometry-guided and rigorous tethered (bond-restrained).

Network pharmacology
A complete, guided workflow: map a compound (or several) and a disease to their shared targets, build the STRING protein–protein interaction network, rank hub genes, and run GO/KEGG enrichment—with multi-compound and multi-disease modes. Connects to public databases (Open Targets, DGIdb, ChEMBL, STRING, Enrichr).

From hub genes to docking
Top hub genes are automatically matched to a representative PDB structure (or an AlphaFold model) and sent, docking-ready, into the docking workspace with the search box pre-centred on the co-crystallised ligand—including for covalent targets.

Trusted docking engine
AutoDock Vina 1.2 with selectable Vina / Vinardo scoring and adjustable exhaustiveness.

Smart preparation
Fetch receptors by PDB ID or upload; keep waters/ions if needed; ligands from SMILES, SDF, MOL2, MOL or PDB, protonated at a chosen pH.

Rich interaction analysis
Automatic 2D interaction diagrams and an interactive 3D viewer (H-bonds, contacts, distances, and the covalent bond), exported as high-resolution images.

Virtual screening
Dock a whole library, rank hits by affinity with drug-likeness filters, inspect every compound and export to CSV—including an optional covalent-binder screening mode.

Publication-ready figures & reports
Export every network, Venn diagram, enrichment plot and hub-gene figure as high-resolution PNG or vector SVG, plus one-click PDF reports and CSV data for the full network-pharmacology analysis.

MD-ready export
One-click, self-contained preparation packages for AMBER, CHARMM and GROMACS, plus PDB complexes and formatted reports.

Quick structure cleanup
Optional one-click energy minimization to relieve clashes and tidy a docked pose, with no atom-typing hassle.

Private and cross-platform
Everything runs locally on Windows and macOS, with no account and no upload.

Download and installation

Windows

Download DrugDesignStudio-Setup.exe from the download folder.
Double-click the installer and follow the prompts.
If Windows SmartScreen appears --> choose "More info" then "Run anyway".
Launch Drug Design Studio from the Start menu.

Requires Windows 10 or 11 (64-bit). The docking engine is bundled, so there is no extra setup.

macOS

Download Drug-Design-Studio-macOS.dmg from the download folder.
Open the disk image and drag DDS to Applications.
First launch: right-click the app and choose Open (or approve it in System Settings, Privacy and Security).
DDS opens straight into the workspace.

Requires macOS 12 (Monterey) or later. Universal build for Apple-silicon and Intel Macs. All built-in, no extra setup.

System requirements

Operating system: Windows 10/11 or macOS 12+
Processor: any modern multi-core CPU
Memory: 8 GB (16 GB recommended)
Disk: about 2 GB for the app and engine
Network: required for the network-pharmacology module (which queries public databases such as Open Targets, ChEMBL, STRING and Enrichr), to fetch PDB structures, and for optional AI features; the docking workflow runs fully offline

DDS Release Notes:

To stay informed about new releases, follow the version numbers and release dates below. DDS is under active, ongoing development, with further enhancements planned.

Version Release Date Update Details

V1.0 10/06/2026 Initial public release (Docking/VS)

V2.0 26/06/2026 Added Network Pharmacology Module

V3.0 under development QSAR/3D QSAR Module

Citing DDS

If DDS supports your research, please cite:

1. Mahmoud E Soliman, Drug Design Studio (DDS): An all-in-one Cross-Platform for Covalent/Non-Covalent Docking, Covalent Binders Virtual Screening and Protein-Ligand interaction analysis - Under Review

2. Mahmoud E Soliman, Drug Design Studio (DDS) 2.0: A Unified Platform for Network Pharmacology Integrated with Docking and Virtual Screening Workflow for Covalent/Non-Covalent Binders - (https://www.preprints.org/manuscript/202607.2122)

DDS is developed and designed by Prof. Mahmoud E. Soliman, Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, South Africa.
For reporting or feedback: Email Prof. M. Soliman at soliman@ukzn.ac.za