Directed evolution of proteins in sequence space with gradients

🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)

Inference code for PoET: A generative model of protein families as sequences-of-sequences

🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).

Interpretable genotype-phenotype landscape modeling

PyPEF – Pythonic Protein Engineering Framework

Automancer is a software application that enables researchers to design, automate, and manage their experiments.

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

PLMFit platform for TL on PLMs

A curated list of awesome protein design research, software and resources.

PyPEF – Pythonic Protein Engineering Framework

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)

Code, data and notebooks for engineering enzymes with ultra-high throughput microfluidics. Please read our accompanying paper for details.

How to build a large dataset of enzyme variants to evaluate enzyme design algorithms

Nucleotide augmentation for machine learning-guided protein engineering (https://doi.org/10.1093/bioadv/vbac094, 2022)

Developing classification models for DNA-Binding proteins through machine learning and large language models

Phage library sequence generator with degenerate basepairs.

De novo enzyme design of oxirane:NAD(P)H reductase enzyme

Open-source synthetic fusion protein for self-healing textiles. Built with AI, powered by biology.