Directed evolution of proteins in sequence space with gradients
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Aug 6, 2024 - Jupyter Notebook
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protein-engineering
Here are 22 public repositories matching this topic...
Inference code for PoET: A generative model of protein families as sequences-of-sequences
deep-learning proteins generative-model protein-sequences protein-engineering protein-language-model
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Apr 24, 2024 - Python
Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2024).
protein-structure protein zero-shot protein-engineering graph-neural-networks directed-evolution mutant-prediction
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Oct 24, 2024 - Python
Interpretable genotype-phenotype landscape modeling
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Dec 3, 2023 - Python
Augmenting zero-shot mutant prediction by retrieval-based logits fusion.
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Nov 16, 2024 - Python
PyPEF – Pythonic Protein Engineering Framework
machine-learning regression python3 protein-sequences protein-engineering in-silico protein-fitness-prediction
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Dec 13, 2024 - Python
Automancer is a software application that enables researchers to design, automate, and manage their experiments.
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Jul 26, 2023 - Python
PyPEF – Pythonic Protein Engineering Framework
machine-learning regression python3 protein-sequences protein-engineering in-silico protein-fitness-prediction
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Dec 13, 2024 - Python
Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing
enzyme mutation protein fitness-landscape crispr-cas9 protein-engineering base-editing llm large-language direct-evoluation direct-evolution large-langage-models
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Jun 6, 2024 - Jupyter Notebook
A curated list of awesome protein design research, software and resources.
bioinformatics structural-biology protein-structure molecular-biology protein-design protein-protein-interaction protein-sequence structural-bioinformatics protein-engineering protein-folding protein-structure-prediction bioinformatics-tool protein-function alphafold alphafold2 alphafold-multimer
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May 10, 2022
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
bioinformatics structural-biology protein-structure drug-discovery molecular-evolution protein-sequence protein-engineering molecular-modeling molecular-docking alphafold molecular-generation alphafold2
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Jul 21, 2022
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)
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Aug 26, 2024 - Jupyter Notebook
How to build a large dataset of enzyme variants to evaluate enzyme design algorithms
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Mar 11, 2024 - Jupyter Notebook
Code, data and notebooks for engineering enzymes with ultra-high throughput microfluidics. Please read our accompanying paper for details.
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Nov 27, 2024 - Jupyter Notebook
Nucleotide augmentation for machine learning-guided protein engineering (https://doi.org/10.1093/bioadv/vbac094, 2022)
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Feb 3, 2023 - Python
PLMFit platform for TL on PLMs
ai pytorch transfer-learning plm fine-tuning protein-engineering pytorch-lightning downstream-tasks deepspeed protein-language-models
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Dec 10, 2024 - Python
Phage library sequence generator with degenerate basepairs.
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Mar 14, 2023 - Python
De novo enzyme design of oxirane:NAD(P)H reductase enzyme
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Dec 19, 2015 - Groff
Developing classification models for DNA-Binding proteins through machine learning and large language models
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Dec 11, 2024 - Jupyter Notebook
Directed Evolution in Silico
bioinformatics julia protein-sequences dna-sequences protein-engineering rna-sequences ml-de directed-evolution
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May 13, 2024 - Julia
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