DDS
Drug Design Studio (DDS)
Covalent and Non-covalent Docking & Virtual Screening · Network Pharmacology · 3D-QSAR & Pharmacophore Modelling · Nano-Biopharmaceutical Modelling
A single, guided, cross-platform desktop application that brings four complementary drug-design workflows together behind one sleek, easy-to-use interface. Free, no coding required, with the docking workflow running fully offline.
Download for Windows and macOS Covalent & non-covalent docking & virtual screening | Network pharmacology | 3D-QSAR & pharmacophore modelling | Nano-biopharmaceutical modelling
What is DDS?
Drug Design Studio (DDS) removes the barrier of juggling several separate programs for a drug-discovery workflow. It is a single, guided desktop application, built around simplicity and integrating trusted open-source engines (AutoDock Vina, RDKit, Meeko, Open Babel and 3Dmol.js). DDS comprises four integrated modules:
- Docking & virtual screening. Covalent and non-covalent molecular docking and whole-library virtual screening, from a protein structure to ranked, annotated, publication-ready results.
- Network pharmacology. Maps 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 docking.
- 3D-QSAR & pharmacophore modelling. Ligand-based activity prediction with validated QSAR / 3D-QSAR and pharmacophore models, feeding top candidates into structure-based screening.
- Nano-biopharmaceutical modelling. Molecular-level modelling of drug encapsulation and complexation for nanocarrier–drug and drug–drug systems.
Systems-level, ligand-based, structure-based and nano-formulation analyses therefore all live in one application, feeding cleanly into downstream molecular-dynamics studies.
The four modules
MODULE 1
Docking & virtual screening
Covalent and non-covalent docking (AutoDock Vina 1.2, Vina / Vinardo scoring, adjustable exhaustiveness) and whole-library virtual screening with drug-likeness filters. A built-in covalent mode adds automatic warhead detection, interactive reactive-residue targeting, and two protocols—fast geometry-guided and rigorous tethered (bond-restrained).
MODULE 2
Network pharmacology
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. Top hub genes are auto-matched to a representative PDB (or AlphaFold) structure and sent, docking-ready, into Module 1. Uses Open Targets, DGIdb, ChEMBL, STRING and Enrichr.
MODULE 3
3D-QSAR & pharmacophore modelling
Ligand-based activity prediction: build and validate QSAR / 3D-QSAR and pharmacophore models with molecular descriptors, cross-validation, Y-scrambling and applicability-domain checks, then send the top-ranked candidates straight into docking and virtual screening.
MODULE 4
Nano-biopharmaceutical modelling
Model drug encapsulation and complexation at the molecular level—host–guest inclusion complexes and drug–drug / drug–excipient complexation. DDS assembles the complex, runs a conformational/orientational search, and computes the interaction energy (van der Waals, electrostatic and solvation) with 2D/3D interaction maps—validated against documented complexes, with pre-loaded examples.
Other capabilities
Cross-module hand-offs
Prioritised targets flow between modules in one application: network-pharmacology hub genes and top QSAR candidates are sent, docking-ready, straight into docking and virtual screening.
Smart structure 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.
Publication-ready figures & reports
Export networks, Venn diagrams, enrichment plots, hub-gene figures and interaction maps as high-resolution PNG or vector SVG, plus one-click PDF reports and CSV data.
MD-ready export
One-click, self-contained preparation packages for AMBER, CHARMM and GROMACS, plus PDB complexes and formatted reports.
Private and cross-platform
Everything runs locally on Windows and macOS, with no account and no upload; the docking, QSAR and nano workflows run fully offline.
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, QSAR and nano workflows run 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 Update Details
V1.0 Initial public release (Docking/VS)
V2.0 Added Network Pharmacology Module
V3.0 Added 3D-QSAR & Pharmacophore Modelling Module
V4.0 Added Nano-biopharmaceutical Modelling Module
V4.1 Several enhancements
Citing DDS If DDS supports your research, please cite:
1. Mahmoud E. Soliman. Drug Design Suite (DDS) 2.0: A Unified Platform for Network Pharmacology Integrated with Docking and Virtual Screening Workflow for Covalent/Non-Covalent Binders — International Journal of Molecular Sciences — accepted (https://www.preprints.org/manuscript/202607.2122)
2. 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).
3. Mahmoud E. Soliman. Drug Design Studio (DDS) 3.0: A Streamlined QSAR, 3D-QSAR and Pharmacophore Modelling Platform Coupling Ligand-Based Activity Prediction to Covalent and Non-Covalent Structure-Based Discovery. (Under review).
4. Mahmoud E. Soliman. Drug Design Studio (DDS) 4.0: A Nanopharmaceutical Simulation Platform for Automated Modelling of Drug–Nanocarrier Encapsulation and Drug–Drug Complexation. (Under review).
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