GitHub topics: protein-engineering
ai4protein/VenusREM
🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)
Language: Python - Size: 359 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 69 - Forks: 8
espjose/BioPatch-SelfHealing-Protein
Open-source synthetic fusion protein for self-healing textiles. Built with AI, powered by biology.
Size: 13.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0
Protein-Engineering-Framework/PyPEF
PyPEF – Pythonic Protein Engineering Framework
Language: Python - Size: 148 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 24 - Forks: 3
niklases/PyPEF
PyPEF – Pythonic Protein Engineering Framework
Language: Python - Size: 268 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 14 - Forks: 2
OtoYuki/proteus
Proteus: A Django-based web application for a semi-automated computational pipeline in synthetic protein design, integrating ColabFold, GROMACS, and ML ranking.
Language: JavaScript - Size: 2.8 MB - Last synced at: about 10 hours ago - Pushed at: about 18 hours ago - Stars: 0 - Forks: 0
Sanofi-Public/prodigyprotein
Protein Diversification and Generation through Yielded mutations (Prodigy) Protein is an end-to-end platform for plug and play protein engineering
Language: Python - Size: 1010 KB - Last synced at: 7 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
LSSI-ETH/plmfit
PLMFit platform for TL on PLMs
Language: Python - Size: 171 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 16 - Forks: 2
ai4protein/ProtSSN
🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).
Language: Python - Size: 33.1 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 64 - Forks: 6
soldatmat/PELLM
Protein engineering with large language models
Language: Jupyter Notebook - Size: 18.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
NREL/EvoProtGrad
Directed evolution of proteins in sequence space with gradients
Language: Jupyter Notebook - Size: 9.5 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 85 - Forks: 12
Jack-of-AllTrades/BioPatch-SelfHealing-Protein
Open-source synthetic fusion protein for self-healing textiles. Built with AI, powered by biology.
Size: 13.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
johnnytam100/awesome-protein-design
A curated list of awesome protein design research, software and resources.
Size: 29.3 KB - Last synced at: 22 days ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 1
OpenProteinAI/PoET
Inference code for PoET: A generative model of protein families as sequences-of-sequences
Language: Python - Size: 772 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 71 - Forks: 3
Achi-lleas/Computational-Project-McConnell-and-Blanchard-Scaffolds-Hackel-Lab
A protein engineering project that involves the analysis of protein scaffolds and their interaction with other protein targets.
Language: Python - Size: 8.38 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
wudangt/awesome-molecular-modeling-and-drug-discovery
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
Size: 51.8 KB - Last synced at: 22 days ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 0
COLA-Laboratory/GBFLAT
The graph-based fitness landscape analysis framework
Language: Python - Size: 972 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
ProteinEngineering-PESB2/RUDEUS
Developing classification models for DNA-Binding proteins through machine learning and large language models
Language: Jupyter Notebook - Size: 18 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0
Hollfelder-Lab/lrDMS-IRED
Code, data and notebooks for engineering enzymes with ultra-high throughput microfluidics. Please read our accompanying paper for details.
Language: Jupyter Notebook - Size: 36.4 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 6 - Forks: 0
ProteinEngineering-PESB2/numerical_representations_protein_seqs
Exploring digital signal processing combined with physicochemical properties support by NLP techniques
Language: Python - Size: 430 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1
vector-engineering/fit4function
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)
Language: Jupyter Notebook - Size: 70 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0
westlake-repl/ProteinLM-TDG2-Mutation
Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing
Language: Jupyter Notebook - Size: 7.8 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 11 - Forks: 1
ProteinEngineering-PESB2/hfbs-class-models
Developing assembled functional classifications models via optimized machine learning algorithms
Language: Python - Size: 361 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1
soldatmat/DESilico.jl
Directed Evolution in Silico
Language: Julia - Size: 81.1 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
retospect/phagetrix
Phage library sequence generator with degenerate basepairs.
Language: Python - Size: 70.3 KB - Last synced at: 20 days ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0
dacarlin/bagel-project
Complete lab and computational undergraduate-level course that teaches students how to design and test novel enzymes in the lab
Language: Jupyter Notebook - Size: 2.34 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 2
usnistgov/lantern
Interpretable genotype-phenotype landscape modeling
Language: Python - Size: 1.85 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 33 - Forks: 5
ProteinEngineering-PESB2/XAI_for_pi
Exploring XAI methods for protein engineering applications
Language: Jupyter Notebook - Size: 3.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
dacarlin/boxi
De novo enzyme design of oxirane:NAD(P)H reductase enzyme
Language: Groff - Size: 37.6 MB - Last synced at: over 1 year ago - Pushed at: over 9 years ago - Stars: 2 - Forks: 1
adaptyvbio/automancer
Automancer is a software application that enables researchers to design, automate, and manage their experiments.
Language: Python - Size: 2.82 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 0
minotm/NTA
Nucleotide augmentation for machine learning-guided protein engineering (https://doi.org/10.1093/bioadv/vbac094, 2022)
Language: Python - Size: 7.51 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1
