Discovery + Design
Structure Editor
Draw or paste a molecule once and reuse it across ChemistryAtlas tools.
ChemistryAtlas Apps Hub
Generative molecular design and advanced chemistry AI tools
Browse ChemistryAtlas generative molecular design tools for molecule generation, property-constrained design, virtual libraries, docking and active-learning screening, ChemProp-style prediction, MolPAL workflows, and model connectors.
These apps are the pro tier for ideation, library growth, multi-objective scoring, and AI-assisted molecule optimization.
Generative Molecular Design Pro
These apps are the pro tier for ideation, library growth, multi-objective scoring, and AI-assisted molecule optimization.
What this hub covers
The Generative Molecular Design Pro hub focuses on advanced AI workflows: target-conditioned molecule generation, virtual library enumeration, active-learning screening, docking connectors, ChemProp-style property models, and model-backed design loops.
Common workflows
- Generate or enumerate candidate molecules under property, substructure, scaffold, or reaction constraints.
- Score candidate libraries with QSAR, ChemProp, docking, active-learning, and multi-property screens.
- Connect sidecar generative, prediction, and screening environments without bloating the main web backend.
Related ChemistryAtlas pages
Featured tools in this workflow
Discovery + Design
Similarity + Substructure Search
Run RDKit Morgan-fingerprint similarity and SMILES/SMARTS substructure matching over a pasted or uploaded library.
Discovery + Design
Retrosynthesis Planner
Detect common retrosynthetic disconnections such as esters, amides, aryl halides, and boronic-acid coupling handles.
Discovery + Design
Forward Reaction / Product Predictor
Apply RDKit reaction SMARTS templates for amide, ester, and hydrogenation product prediction.
Discovery + Design
Scaffold + R-Group Analyzer
Extract Murcko scaffolds and scaffold atom counts from names or SMILES with RDKit.
Discovery + Design
Generative Molecular Design
Enumerate and rank substituent designs against MW, TPSA, and target-logP constraints.
Discovery + Design
Matched Molecular Pairs Analyzer
Build pairwise SAR delta tables with Murcko scaffold checks, Tanimoto similarity, and property changes.
Discovery + Design
Diversity / Cluster Selection
Select diverse compounds by greedy max-min distance over RDKit Morgan fingerprints.
Discovery + Design
Virtual Library Enumerator
Enumerate R-group or reaction-SMARTS virtual libraries, calculate product descriptors, and export SDF/CSV.
Discovery + Design
Molecule -> Materials Bridge
Screen molecular precursors for linker, electrolyte, chromophore, and organic-electronics motifs.
Generative Molecular Design Pro
Target-Property Molecule Generator
Generate candidates toward logP, MW, TPSA, solubility, pKa, ADMET, or custom property goals.
Generative Molecular Design Pro
Scaffold Hopping Designer
Propose scaffold replacements that preserve property profile while changing core structure.
Generative Molecular Design Pro
R-Group Optimization Pro
Enumerate and rank substituent replacements using RDKit descriptors, synthesis filters, and optional ChemProp predictions.
Generative Molecular Design Pro
Multi-Objective Molecular Optimizer
Optimize candidate molecules across potency proxy, solubility, alerts, diversity, novelty, and synthesis feasibility.
Generative Molecular Design Pro
Synthesis-Aware Molecule Generator
Generate molecules and require route/template feasibility before ranking final candidates.
Generative Molecular Design Pro
Matched Pair Design Suggestions
Suggest medicinal-chemistry transformations and property-direction changes from matched-pair rules.
Generative Molecular Design Pro
Active-Learning Molecular Design Loop
Upload measured data and candidates, train a local model, and recommend next molecules to make/test.
Generative Molecular Design Pro
Generative Library Builder
Build focused virtual libraries from cores, R-groups, reaction handles, and property constraints.
Generative Molecular Design Pro
ChemProp Model Builder Pro
Train property models using ChemProp sidecar when available or local RDKit Random Forest fallback.
Generative Molecular Design Pro
ChemProp Batch Predictor
Run batch molecular property prediction with saved ChemProp models or local descriptor fallback.
Generative Molecular Design Pro
ChemProp Uncertainty / Applicability Domain
Estimate uncertainty and applicability domain from ensemble/model spread or fingerprint distance fallback.
AI Spectra + Virtual Screening
AI MS/MS Predictor
Predict MS/MS fragments using ms-pred/ICEBERG sidecar when available or deterministic exact-mass losses locally.
AI Spectra + Virtual Screening
Spectrum Similarity Scorer
Score experimental vs predicted/library spectra with cosine similarity and matched-peak diagnostics.
AI Spectra + Virtual Screening
Candidate Structure Ranker
Rank candidate structures against formula, exact mass, spectrum hits, fragments, and property filters.
AI Spectra + Virtual Screening
Formula + Spectrum Elucidation
Combine formula constraints and MS/MS similarity to produce structure-elucidation candidate reports.
AI Spectra + Virtual Screening
PyScreener Docking Workflow
Prepare a docking workflow and call PyScreener sidecar when configured; otherwise emit runnable docking manifests.
AI Spectra + Virtual Screening
MolPAL Active-Learning Virtual Screening
Plan or run MolPAL-style active-learning virtual screening from docking scores and candidate libraries.
AI Spectra + Virtual Screening
Protein/Ligand Prep Checklist
Generate a protein/ligand preparation checklist for docking, protonation, waters, cofactors, grid box, and controls.
AI Spectra + Virtual Screening
Docking Result Ranker
Rank docking results with score, ligand efficiency, strain, alerts, diversity, and interaction notes.
AI Spectra + Virtual Screening
Docking-to-Design Loop
Convert docking hits into next design ideas with R-group/scaffold suggestions and active-learning priorities.