AI agent toolkit: unified LLM API, agent loop, TUI, coding agent CLI

Pi extension: a persistent second model that reviews the main agent's work each turn and injects concise advice inline.

SGX-ready Enclaive Docker Image for Nginx

High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings

Fast, lightweight reaction classification with high granularity

MolBench — a molecular-visualization benchmark & harness for CI (LLM) assistants: natural language → Mol*/ipymolstar API calls, graded deterministically, plus VLM-judged visual tasks.

Mol* chat-driver: natural-language prompts -> MolViewSpec scenes rendered in Mol*, with reliable prompt/feedback capture. Built for MolBench human evaluation. Free for non-commercial use.

Preliminary model report for the OpenADMET PXR Challenge

An Open-source Drug Discovery Engine

Code used to mine surfaces.

A smarter cd command. Supports all major shells.

Codebase for NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products

DockStream: A Docking Wrapper to Enhance De Novo Molecular Design

Towards Generalizable Protein-ligand Co-folding with ACER (Adaptive Co-folding via pocket Exploration and pose Ranking)

Flexible alignment of molecules using SENSAAS

Shape-based alignment of molecules using 3D point-based representation

LIVIA (Local Interaction VIsualization and Analysis) — Analyze and visualize protein interaction interfaces from structure predictions. Browser-based, supports all major prediction platforms.

The Modular and Open-source Implicit Solvation Toolkit (MOIST)

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema as…

Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert.

ApoSight is CLI based that converts apo AlphaFold structures into docking-ready binding-site definitions. It combines RCSB template discovery, strict/interactive selection, two-pass pocket transfer…