BoltzGen: Toward Universal Binder Design
A graph-based python framework for fitness landscape analysis
Claude Code skills for protein design
🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)
AI-powered biologics design campaign agent — multi-agent orchestration with BoltzGen, PXDesign, Protenix, and 200+ cloud tools. Antibodies, nanobodies, de novo binders, and beyond.
Inference code for PoET: A generative model of protein families as sequences-of-sequences
Directed evolution of proteins in sequence space with gradients
🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).
Official implementation of μProtein -- Accelerating protein engineering with fitness landscape modeling and reinforcement learning
Optimization framework for AI-guided protein engineering
Interpretable genotype-phenotype landscape modeling
Structural biology superpowers for AI coding agents: PyMOL, ChimeraX, AlphaFold DB, RCSB PDB, UniProt, and Rosetta workflows.
Automancer is a software application that enables researchers to design, automate, and manage their experiments.
PyPEF – Pythonic Protein Engineering Framework
PLMFit platform for TL on PLMs
Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing
A curated list of awesome protein design research, software and resources.
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)
PyPEF – Pythonic Protein Engineering Framework
Propose CDR single-point mutations that rescue antibody expression without disrupting antigen binding, using bound vs. unbound ProteinMPNN logit analysis.
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