Directed evolution of proteins in sequence space with gradients
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Oct 18, 2025 - Jupyter Notebook
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directed-evolution
Here are 15 public repositories matching this topic...
🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).
protein-structure protein zero-shot protein-engineering graph-neural-networks directed-evolution mutant-prediction
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Apr 10, 2026 - Python
Protein Design by Machine Learning guided Directed Evolution
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Jan 1, 2026 - Python
LatentDE: Latent-based Directed Evolution for Protein Sequence Design
evolutionary-algorithm gradient-ascent variational-autoencoder protein-language-model directed-evolution protein-optimization
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Apr 2, 2025 - Python
TeBaAb: Text-Based Antigen-Conditioned Antibody Redesign via Directed Evolution
natural-language-processing evolutionary-algorithm protein-design variational-autoencoder protein-language-model directed-evolution antibody-design binding-affinity-prediction
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Jun 10, 2026 - Python
Computational model of laboratory directed evolution + experiments.
evolutionary-computation digital-evolution directed-evolution artificial-selection parent-selection-algorithms
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Jun 29, 2022 - Python
Learning to Solve Multiresolution Matrix Factorization by Manifold Optimization and Evolutionary Metaheuristics
evolutionary-algorithms wavelet-transform graph-convolutional-network graph-wavelet matrix-factorisation multiresolution-analysis stiefel-manifold-optimization directed-evolution
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Apr 17, 2026 - Python
Directed Evolution of Proteins via Bayesian Optimization in Embedding Space
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May 2, 2025 - 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
GenLoop — a closed generative drug-design loop on dtSFM; directed evolution of small molecules (Reddy 2026). Generate → encoder-rerank → AlphaFold-3 verify → LoRA-refine.
cheminformatics drug-discovery generative-models alphafold drug-target-interaction directed-evolution foundation-model
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Jun 10, 2026 - Python
Unified Python library and CLI for protein structure prediction and inverse folding.
python cli bioinformatics deep-learning structural-biology transformers computational-biology pytorch protein-design inverse-folding protein-structure-prediction alphafold2 alphafold-multimer directed-evolution esmfold esm2 esm-if proteinmpnn ligandmpnn ai4protein
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Feb 16, 2026 - Python
ProtEvolveLab — Interactive Protein Language Model & In-Silico Directed Evolution Laboratory. 6 modules: amino acid embeddings, NK fitness landscapes, directed evolution simulator, epistasis mapper, MCTS protein designer, strategy arena. Zero dependencies.
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Jun 5, 2026 - HTML
Generates randomly generated fastQ files from a template and upstream sequence.
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Apr 4, 2024 - Python
Calculates the probability of finding the top variant in a library of sequences.
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Mar 29, 2024 - Python
A protocol for directed code evolution orchestration, with a reference implementation and conformance suite
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Jun 16, 2026 - Python
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