V-LiSEMOD Workspace

Explore viral protein-ligand structures, surface exposure, and degrader-readiness evidence from one curated workspace.

Select a virus, choose a PDB structure, inspect the bound ligand, and generate PyMOL sessions, ligand imagery, or query-ready outputs without leaving the V-LiSEMOD environment.

Select virus Select PDB Select ligand Generate visual and query outputs

Start a ligand analysis session Browse by protein target Learn about V-LiSEMOD

Visual Overview

See the complete V-LiSEMOD structure-to-design workflow.

The graphical abstract summarizes how the platform connects viral structures, interaction evidence, solvent exposure, linkability, PROTACability, and downstream design handoff.

01 Viral structures 02 Interaction analysis 03 Solvent-exposed atoms 04 Warhead linkability 05 PROTACability triage 06 Design handoff

Workflow Modules

Move between structure query, ligand comparison, and design triage in one workflow.

Core Query

Protein Query

Filter curated viral structures by virus, protein class, and ligand to build export-ready structure sets.

Open Protein Query

Ligand First

Ligand Indexer

Start from a ligand code or synonym and locate mapped PDB-chain-residue contexts.

Open Ligand Indexer

Comparative Analysis

Ligand Comparison

Compare ligand interaction signatures across PDB structures and inspect warhead-relevant ligand contexts.

Open Comparison

Evidence Triage

PROTACability

Review warhead linkability, target lysine accessibility, structure priority, and degrader-readiness heuristics.

Open PROTACability

External Handoff

PROTAC Builder

When you move from viral ligand analysis into degrader design, continue in the standalone external builder.

Open PROTAC Builder ↗

Primary Workflow

Generate a V-LiSEMOD analysis session

Choose a virus, structure, and ligand to prepare a PyMOL session, inspect solvent exposure, and export ligand-focused visuals from the same starting point.

1. Virus 2. PDB 3. Ligand 4. Output

Select Virus:

Select PDB Code:

Select Ligand:

Binding Pocket Capture residues within 5 Angstroms of the selected ligand for structure review. Shrake-Rupley SASA Highlight solvent-exposed ligand atoms using a 1.4 Angstrom probe radius. Functional Group Atoms Expose functional-group level objects when ligand annotations are available.

Project resources

Learn more without leaving the workflow

Explore methods, use cases, viral PROTAC design context, collaboration, and citation guidance.