williamTLmiller/millerbind-open-v1

Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.

197 bioinformatics and life science skills for Claude Code and AI agents, achieving 92.0% accuracy on BixBench. Covers RNA-seq, single-cell analysis, drug discovery, proteomics, and more. Powers OmicsHorizon (195+ stars, 2026)

Inflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.

Nesso-1 is a fast, structure-based protein–ligand binding-affinity model. Given a protein sequence and a ligand (SMILES / CCD code / SDF), it predicts a binding affinity scalar along with a binder/non-binder score.

Plant Compound Extractor is a desktop application that builds a ready-to-use, deduplicated library of 3D ligand structures for a given plant. It queries multiple natural-product and chemical databases (COCONUT, LOTUS, Wikidata, PubChem, PlantaeDB, USDA Dr. Duke's, KNApSAcK and IMPPAT) in parallel, resolves each compound against PubChem for a canonical structure, and falls back to direct source retrieval when needed. Retrieved structures are then converted to 3D using RDKit, with configurable conformer generation and physicochemical filters (molecular weight, rotatable bonds, ring size, etc.). It can also process a manually supplied compound list, or convert an existing folder of 2D structures to 3D.