ArticleInternational journal of molecular sciences2026
Drug Design Studio (DDS) 2.0: A Unified Platform for Network Pharmacology Integrated with Docking and Virtual Screening Workflow for Covalent/Non-Covalent Binders.
Article in International journal of molecular sciences, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist "one drug, one target" view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains fragmented and technically demanding: researchers must query several independent databases, install and reconcile multiple standalone tools for target collection, network construction, hub-gene ranking and pathway enrichment, and then manually bridge the results into structure-based follow-up such as molecular docking. This fragmentation is a persistent barrier, particularly for experimental and non-specialist users. Here, we present the network-pharmacology module of Drug Design Studio (DDS) 2.0, a unified, user-friendly platform that streamlines the entire workflow-disease target retrieval, compound-target prediction, shared-target identification, protein-protein interaction (PPI) network construction, hub-gene ranking and Gene Ontology/pathway enrichment-within a single guided interface, consolidating steps that otherwise require several separate tools. Crucially, DDS 2.0 links the resulting hub genes directly to the docking and virtual-screening engine introduced in the previous DDS releases: representative experimental structures and mutant forms-for instance, resistance-conferring variants found in drug-resistant strains-of the target proteins are selected and streamed into a docking-ready workspace, with dedicated support for covalent binders. We validate the module against four independent published network-pharmacology studies spanning diverse diseases; DDS reproduces the reported hub genes with a mean recovery (recall) of 0.85 (range 0.80-0.90) and a mean Jaccard index of 0.74, and recovers the corresponding target sets and enriched pathways. DDS 2.0 thus delivers an integrated route from systems-level analysis to structure-based drug design. DDS 2.0 is freely and publicly accessible. Comprehensive user documentation is built directly into DDS and can be accessed at any time from the Documentation panel.
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