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directed-evolutionHere are 24 public repositories matching this topic...Language: All
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A graph-based python framework for fitness landscape analysis
python bioinformatics computational-biology epistasis black-box-optimization fitness-landscape combinatorial-optimization fitness-landscape-analysis deep-mutational-scanning evolutionary-biology protein-engineering directed-evolution
Directed evolution of proteins in sequence space with gradients
🧬 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
Protein Design by Machine Learning guided Directed Evolution
LatentDE: Latent-based Directed Evolution for Protein Sequence Design
evolutionary-algorithm gradient-ascent variational-autoencoder protein-language-model directed-evolution protein-optimization
🧬 A general harness enhances zero-shot fitness predition for any protein foundation model.
protein harness protein-design inverse-folding protein-engineering protein-language-model directed-evolution training-free protein-foundation-models
Computational model of laboratory directed evolution + experiments.
evolutionary-computation digital-evolution directed-evolution artificial-selection parent-selection-algorithms
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
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
Generates randomly generated fastQ files from a template and upstream sequence.
bioinformatics ngs next-generation-sequencing python3 random-generation fastq mock-data ngs-analysis synthetic-data dna-sequencing ngs-pipeline phred-quality-scores mock-data-generator quality-scores directed-evolution mock-data-repository
Directed Evolution of Proteins via Bayesian Optimization in Embedding Space
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
Directed Evolution in Silico
bioinformatics julia protein-sequences dna-sequences protein-engineering rna-sequences ml-de directed-evolution
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
Calculates the probability of finding the top variant in a library of sequences.
Sequence Space Coverage Calculator
python bioinformatics julia synthetic-biology computational-biology mutagenesis sequence-analysis protein-engineering library-design directed-evolution
Can an AI evolve a brighter protein? Scored against real lab data, round by round
bioinformatics typescript deep-mutational-scanning protein-engineering cloudflare-workers directed-evolution esm2
Prior- and constraint-driven directed-evolution agent on the GB1 four-site landscape: seven-arm controlled comparison, auditable constraints, and an honest null result for the LLM
reproducible-research computational-biology active-learning interpretability protein-engineering directed-evolution ai-for-science llm-agent gb1 protein-fitness-landscape
Active learning over real protein fitness landscapes: GP-UCB vs random under a fixed experiment budget, replicated multi-seed on GB1 and AAV2. Snakemake DAG + provenance.
A trial of whether life could be built on silicon rather than carbon — and an honest verdict of suspension.
open-access essay titan astrobiology abiogenesis directed-evolution planetary-habitability silicon-based-life alternative-biochemistry organosilicon-chemistry
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