protein-engineering

There are 4 repositories under protein-engineering topic.

NREL / EvoProtGrad
Directed evolution of proteins in sequence space with gradients
directed-evolution huggingface mcmc protein-engineering protein-language-model
Language:Jupyter Notebook 76
OpenProteinAI / PoET
Inference code for PoET: A generative model of protein families as sequences-of-sequences
deep-learning generative-model protein-engineering protein-language-model protein-sequences proteins
Language:Python 53
tyang816 / ProtSSN
Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2024).
directed-evolution graph-neural-networks mutant-prediction protein protein-engineering protein-structure zero-shot
Language:Python 48
usnistgov / lantern
Interpretable genotype-phenotype landscape modeling
bioinformatics machine-learning computational-biology synthetic-biology protein-engineering
Language:Python 35
PyPEF
Protein-Engineering-Framework / PyPEF
PyPEF – Pythonic Protein Engineering Framework
machine-learning protein-sequences protein-fitness-prediction in-silico python3 regression protein-engineering
Language:Python 22
adaptyvbio / automancer
Automancer is a software application that enables researchers to design, automate, and manage their experiments.
automation experimental-design lab lab-automation microfluidics protein protein-engineering
Language:Python 19
PyPEF
niklases / PyPEF
PyPEF – Pythonic Protein Engineering Framework
in-silico machine-learning protein-engineering protein-fitness-prediction protein-sequences python3 regression
Language:Python 13
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
base-editing crispr-cas9 direct-evoluation direct-evolution enzyme fitness-landscape large-langage-models large-language llm mutation protein protein-engineering
Language:Jupyter Notebook 13
johnnytam100 / awesome-protein-design
A curated list of awesome protein design research, software and resources.
alphafold alphafold-multimer alphafold2 bioinformatics bioinformatics-tool molecular-biology protein-design protein-function protein-sequence protein-structure structural-bioinformatics structural-biology protein-engineering protein-folding protein-protein-interaction protein-structure-prediction
11
wudangt / awesome-molecular-modeling-and-drug-discovery
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
molecular-modeling alphafold alphafold2 bioinformatics drug-discovery protein-engineering protein-sequence protein-structure structural-biology molecular-docking molecular-evolution molecular-generation
10
vector-engineering / fit4function
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)
aav machine-learning protein-engineering
Language:Jupyter Notebook 8
dacarlin / bagel-project
How to build a large dataset of enzyme variants to evaluate enzyme design algorithms
protein-engineering machine-learning laboratory-automation benchmarks protein-ai generative-ml
Language:Jupyter Notebook 7
Hollfelder-Lab / lrDMS-IRED
Code, data and notebooks for engineering enzymes with ultra-high throughput microfluidics. Please read our accompanying paper for details.
enzyme enzyme-engineering machine-learning microfluidics protein protein-engineering
Language:Jupyter Notebook 7
minotm / NTA
Nucleotide augmentation for machine learning-guided protein engineering (https://doi.org/10.1093/bioadv/vbac094, 2022)
data-augmentation deep-learning protein-engineering
Language:Python 6
dacarlin / boxi
De novo enzyme design of oxirane:NAD(P)H reductase enzyme
enzyme-design high-performance-computing protein-engineering oxidoreductase rosetta
Language:Groff 2
ProteinEngineering-PESB2 / RUDEUS
Developing classification models for DNA-Binding proteins through machine learning and large language models
dna-binding-proteins machine-learning protein-engineering protein-language-models protein-sequences
Language:Jupyter Notebook 2
retospect / phagetrix
Phage library sequence generator with degenerate basepairs.
codon-optimization degenerate-bases degenerate-primers phage-display protein-engineering
Language:Python 2
soldatmat / DESilico.jl
Directed Evolution in Silico
bioinformatics directed-evolution ml-de protein-engineering dna-sequences protein-sequences rna-sequences julia
Language:Julia 1
ProteinEngineering-PESB2 / hfbs-class-models
Developing assembled functional classifications models via optimized machine learning algorithms
machine-learning protein-encoding protein-engineering protein-function-prediction
Language:Python 0
ProteinEngineering-PESB2 / numerical_representations_protein_seqs
Exploring digital signal processing combined with physicochemical properties support by NLP techniques
machine-learning numerical-representation protein-engineering
Language:Python 0
soldatmat / PELLM
Protein engineering with large language models
bioinformatics directed-evolution ml-de protein-engineering
Language:Jupyter Notebook 0