Directed evolution of proteins in sequence space with gradients

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 2024).

Interpretable genotype-phenotype landscape modeling

PyPEF – Pythonic Protein Engineering Framework

Augmenting zero-shot mutant prediction by retrieval-based logits fusion.

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

PyPEF – Pythonic Protein Engineering Framework

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.

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)

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

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

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

PLMFit platform for TL on PLMs

Directed Evolution in Silico