This page summarizes the methodology behind V-LiSEMOD, including data curation, ligand indexing, interaction analysis, solvent exposure mapping, PyMOL session generation, and PROTACability evidence layers.
V-LiSEMOD organizes viral protein-ligand structures from public structural resources and project curation workflows. The goal is to preserve interpretable links among virus identity, protein target, structure, ligand, chain context, and downstream annotations.
Structures and ligands are indexed to support structure-first, target-first, and ligand-first discovery workflows. This makes it easier to move between PDB identifiers, ligand codes, mapped residue context, and comparative review.
Interaction review layers summarize contacts between viral proteins and bound ligands so users can distinguish conserved interaction anchors from regions that may be more permissive. Arpeggio-style contact data contributes to this interpretation layer when interaction annotations are available.
Ligand atom exposure is evaluated using solvent-accessibility logic consistent with Shrake-Rupley SASA calculations and a 1.4 Angstrom probe radius using the platform’s solvent-exposure workflow. These outputs help highlight ligand atoms that remain more outward-facing in the observed bound pose.
Ligand records may be linked to functional-group and SMILES-based annotations so solvent exposure and atom identity can be interpreted in a chemically meaningful way rather than as isolated atom numbers.
The app can package selected structures, binding-pocket context, and ligand-focused annotations into PyMOL sessions for collaborative visual review, figure preparation, and downstream design discussion.
PROTACability in V-LiSEMOD combines ligand-centered and target-centered evidence, including warhead linkability, solvent exposure, target lysine context, and related structural cues. These are intended as transparent hypothesis-generating layers for triage rather than experimentally validated degradation predictions.
The platform emphasizes traceable structure identifiers, queryable outputs, and reusable visual review artifacts so users can revisit the same structural context and communicate it across collaborators.
Structure-derived annotations do not prove cellular activity, warhead viability, ternary complex formation, ubiquitination, or degradation. Results should be interpreted together with chemistry, assay data, and broader biological context.