🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)
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Apr 25, 2026 - Python
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protein-engineering
Here are 90 public repositories matching this topic...
AI-powered biologics design campaign agent — multi-agent orchestration with BoltzGen, PXDesign, Protenix, and 200+ cloud tools. Antibodies, nanobodies, de novo binders, and beyond.
computational-biology drug-discovery protein-engineering ai-agent antibody-design mcp-server claude-code boltzgen
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Aug 16, 2026 - Python
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 2025).
protein-structure protein zero-shot protein-engineering graph-neural-networks directed-evolution mutant-prediction
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Jul 20, 2026 - Python
Interpretable genotype-phenotype landscape modeling
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Dec 3, 2023 - 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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Sep 6, 2026 - 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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Aug 13, 2025 - Python
PyPEF – Pythonic Protein Engineering Framework
machine-learning regression python3 protein-sequences protein-engineering in-silico protein-fitness-prediction
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Sep 13, 2026 - Python
JAX/Equinox implementation of ProteinMPNN and LigandMPNN for protein sequence design
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Sep 14, 2026 - Python
Structural biology superpowers for AI coding agents: PyMOL, ChimeraX, AlphaFold DB, RCSB PDB, UniProt, and Rosetta workflows.
bioinformatics proteins structural-biology protein-structure computational-biology pymol uniprot rosetta codex protein-design ai-agents protein-engineering molecular-visualization alphafold chimerax claude-code rcsb-pdb alphafold-db pymol-automation chimerax-automation
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Jul 17, 2026 - Python
Analysing Sequence Activity Relationships (SARs) of protein sequences 🔬 and their mutants using Machine Learning. 💻
python machine-learning bioinformatics research-project protein-engineering sequence-function-relationships aaindex sequence-activity-relationships
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Jul 25, 2026 - Python
Protein Diversification and Generation through Yielded mutations (Prodigy) Protein is an end-to-end platform for plug and play protein engineering
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Dec 30, 2025 - Python
Infrastructure for facilitating variant effect prediction using machine learning. Data class to combine assay, sequence, MSA and structure data to a coherent data package. Model cards for supervised and zeroshot ML models.
benchmark proteins protein-engineering computation-biology variant-effect-prediction enzymes protein-fitness-prediction
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Sep 19, 2026 - Python
Nucleotide augmentation for machine learning-guided protein engineering (https://doi.org/10.1093/bioadv/vbac094, 2022)
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Feb 3, 2023 - Python
Protein Language model for AAV capsid generation.
machine-learning reinforcement-learning deep-learning artificial-intelligence drug-discovery protein-engineering capsid-engineering protien-language-model
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May 19, 2026 - Python
Interpretable ranking and layered screening for generated protein backbone candidates.
bioinformatics protein-structure computational-biology protein-design protein-engineering scientific-software rfdiffusion backbone-ranking
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Sep 1, 2026 - Python
AI-agent toolkit for structural biology: design binders, map structures, screen candidates, rank results, and prepare cloud-scale runs.
bioinformatics structural-biology protein-structure computational-biology open-science cloud-computing drug-discovery screening cryo-em protein-design workflow-automation structure-prediction ai-agents protein-engineering protein-folding molecular-modeling runpod agentic-ai binder-design
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Sep 2, 2026 - Python
QC and tag-site scoring for designed protein binders from predicted complexes.
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Sep 3, 2026 - Python
equimol: a library for E(n)-equivariant neural networks for molecular and protein models
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Sep 20, 2026 - Python
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