Starred repositories
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)
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Updated Jun 1, 2026
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…
An open-source agent harness that turns your AI agent into your 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…
This repo contains our customized version of Boltz-2 that conditions the predictive diffusion model on an arbitrary Bayesian likelihood specified by the user.
UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.
Benchmarking tools and analysis scripts for processing and evaluating structural data from the OpenBind EV-A71 2A dataset
Open-source protein-based pharmacophore modeling software
Code and figures related to blogpost "Navigating PXR Chemical Space with High-Throughput Chemistry and Standard-Free Quantification"
Fast, memory-efficient Butina clustering and dataset splitting for chemical fingerprints
Implementation of “Bridging 3D Molecular Structures and Artificial Intelligence by a Conformation Description Language”