Conformer ensembles
Generate and retain candidate conformers so the chosen comparison is not mistaken for the only possible molecular geometry.
Conformer-aware 3D ligand comparison
Inspect the overlay behind every 3D similarity score.
Compare molecular shape, chemical features, and pharmacophore agreement across generated conformers while retaining the reference, selected alignment, scoring components, and applicability of the hypothesis.
3D shape screeningPharmacophoreConformersMolecular overlayFeature similarityScaffold hopping
A score with spatial context
Separate shape overlap from chemical feature agreement.
MolexIO preserves conformer generation, reference identity, selected alignment, shape, color or feature, and pharmacophore components. Scientists can inspect the 3D hypothesis directly and avoid interpreting one consensus number as a complete explanation.
Shape overlap
Compare occupied molecular volume and alignment quality independently from pharmacophoric feature agreement.
Feature similarity
Evaluate donors, acceptors, aromatic, hydrophobic, charged, or other supported feature classes in the aligned geometry.
Pharmacophore evidence
Inspect matched and unmatched spatial features and the reference hypothesis used to define them.
Consensus review
Combine supported 3D signals while retaining each component and avoiding false precision when a component is unavailable.
Downstream testing
Move selected molecules into docking, ADMET, off-target, analog generation, and project-library workflows.
From reference to 3D hypotheses
Use the reference and conformer assumptions explicitly.
- 01
Select the reference
Choose a ligand, conformation, or pharmacophore supported by the question and available evidence.
- 02
Prepare conformers
Generate candidate geometries under documented settings and retain failures or limits.
- 03
Align and score
Evaluate shape and feature components and preserve the selected overlay.
- 04
Inspect and advance
Review 3D agreement and add orthogonal structural, property, and experimental evidence.
Scientific boundary
A good overlay is a spatial hypothesis, not proof of a shared mechanism.
Results depend on conformer coverage, protonation, tautomer and stereochemical state, alignment objective, reference choice, and feature definitions. A pharmacophore match can support prioritization but does not establish a common binding mode, target, affinity, selectivity, or biological activity.
Questions before use
Shape and pharmacophore FAQ
Can shape similarity find different scaffolds?
Yes, but the result depends on conformer sampling, alignment, and whether the reference conformation is biologically relevant.
Does a pharmacophore match prove binding?
No. It is a screening hypothesis based on selected spatial features.
Why inspect the 3D overlay?
It reveals which regions and features agree, which conformer was selected, and where mismatches remain.
Move beyond a single similarity number.
Review conformers, overlays, feature agreement, and the reference hypothesis before advancing a candidate.