A tool that visualizes "inflection points" in LLM generation by generating multiple independent output paths and highlighting low-confidence tokens — moments where the model's output could easily have diverged.
- Generates 3 independent responses per prompt using GEMMA 4 with Top-P/Top-K sampling for diversity
- Highlights tokens with probability < 0.6 in red, marking them as inflection points
- Interactive Gradio GUI with toggleable per-token probability scores and light/dark mode
- See the repo!
- Try the HuggingFace demo!
A conversational CLI agent (powered by Ollama) that takes a plain-English request like "dock dopamine into SULT1A3" and autonomously runs the full workflow: PDB lookup, blind binding-site detection, and AutoDock Vina docking — no prior knowledge of the binding site required.
- Pure-Python buriedness grid scan for pocket detection — no external pocket tool needed
- Proximity fallback: auto-corrects off-target poses using co-crystallized ligand proximity
- Validated on DUD-E receptors (HMGCR, ADRB1, ADRB2, MAOB, DRD2) — true binding site is #1 pocket on all five
- See the repo!
Adversarial molecule optimization from the command line: an Ollama main model designs molecules to bind a protein target while an OpenAI/Anthropic adversary critiques each proposal, with all steps written to a timestamped Markdown report.
- See the repo!
A full-featured CLI version of the MOdular DRug design AGent with rich terminal output, IC50 prediction, and an easy node-integration system for adding new tools.
- Molecular tools: SMILES conversion, similarity search, 3D structure generation, pharmacophore analysis
- Protein tools: UniProt/PDB lookup, ChEMBL bioactives, AutoDock Vina docking, LightGBM IC50 prediction
- Setup script to create a
modragshell alias for use from anywhere - See the repo!
Find background on the quantum mechanics of quantum computing as well as introductions to quantum computing with Q#, Cirq and Qiskit!
- See the repo here!
- Dock molecules is a selction of 6 proteins using the UMA MLIP for all energy evaluations.
- Includes ligand desolvation and strain energy.
- See the repo here!