Antiviral target exploration
Browse viral protein targets and inspect which co-crystal ligands are already available for structure-guided follow-up.
Use Cases
How researchers can use V-LiSEMOD
V-LiSEMOD supports several entry points into viral structure-guided discovery, from target-centric browsing to ligand-first review and degrader-oriented structural triage. Researchers can use the platform to move from a viral target, ligand, or structural question toward clearer evidence, interpretable design logic, and review-ready outputs.
Research workflows
Common ways to work with the platform
These use cases help turn structural data into clearer design discussions, comparison exercises, and review-ready outputs.
Viral ligand structure review
Examine binding context, ligand identity, residue environment, and structure-specific evidence before drawing design conclusions.
Warhead and linkability triage
Review whether a known viral ligand presents chemically interpretable, solvent-facing positions that may merit linker-attachment discussion.
Solvent-exposed atom discovery
Use solvent accessibility and atom-level annotation to separate buried binding atoms from more permissive attachment-vector candidates.
PROTACability screening
Use the structural evidence layers as a hypothesis-generating triage system rather than a validated degradation predictor.
Ligand comparison across PDB structures
Compare how related ligands behave in different binding contexts and inspect interaction burden across structures.
PyMOL session generation
Create visual review packages for team discussion, figure preparation, or medicinal chemistry handoff.
Teaching and demo workflows
Show students or collaborators how structural data informs ligand optimization, solvent exposure reasoning, and careful degrader design triage.
Start points
Choose the workflow that matches your question
V-LiSEMOD is flexible. Start with the tool that matches the question you are trying to answer.
Start with Structure Explorer
Open the main workspace and build a PyMOL-ready structure review session.
Open Structure Explorer →Browse by Protein Target
Search viral proteins, inspect structure coverage, and export target-focused results.
Open Protein Query →Compare Ligands
Review interaction signatures and cross-structure behavior for viral ligands.
Open Ligand Comparison →Review PROTACability
Inspect structural triage evidence for linkerability, lysine context, and follow-up prioritization.
Open PROTACability →
Outputs
What researchers can produce with V-LiSEMOD
Curated structure review
Organize target, ligand, and residue evidence into a more structured review process.
Ligand comparison summaries
Contrast interaction patterns, context dependence, and structure-specific behavior across related ligands.
PyMOL-ready exports
Generate visual review assets that can be shared with collaborators, students, or medicinal chemistry teams.
Design discussion support
Use structure-backed cues to frame follow-up questions around exposure, linkerability, and target-side context.
Teaching-ready visuals
Support demos and learning workflows that show how structural evidence guides chemical reasoning.
Better research navigation
Help users choose the right entry point before they spend time on a deeper structural or design workflow.
Next step
Start with the workflow that best fits your question
V-LiSEMOD works best as an interpretable, structure-guided workspace. Start with the entry point that best matches your current question, then use the outputs to support follow-up discussion, comparison, and design thinking.