An implementation of ESM2 in Equinox+JAX
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Apr 20, 2026 - Python
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esm2
Here are 118 public repositories matching this topic...
End-to-end protein function prediction from structure alone: active sites, binding pockets, GO terms, PPI partners, and drug candidates.
open-source bioinformatics cheminformatics protein-structure computational-biology drug-discovery protein-function-prediction alphafold esm2 active-site-prediction
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May 22, 2026 - Python
Repository of the paper "Exploring sequence landscape of biosynthetic gene clusters with protein language models" published at ICML2024 workshop Machine Learning for Life and Material Science: From Theory to Industry applications
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Apr 25, 2026 - Jupyter Notebook
A reproducible in silico pipeline to rationally design and prioritize anti-Listeria antimicrobial peptides. This workflow integrates sequence generation, physicochemical filtering, ESM-2 embedding and multi-criteria scoring to narrow candidates and reduce experimental burden. Open for community evaluation, modification and further development.
bioinformatics computational-biology protein-design antimicrobial-peptides listeria listeria-monocytogenes protein-language-model esm2
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Oct 21, 2026 - Python
Prediction of anti-fungal proteins using protein language models
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May 8, 2026 - Python
AI-powered protein mutation analysis platform. Enter any UniProt ID, mutate a residue, and SERAPH, an original ESM2+CNN+BiLSTM model, predicts exactly which secondary structures change and why.
machine-learning bioinformatics deep-learning structural-biology nextjs protein-structure computational-biology pytorch bilstm secondary-structure-prediction cnn-bilstm protein-mutations fastapi framer-motion alphafold protein-language-model gemini-ai esm2 mutantscope
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Jul 4, 2026 - Jupyter Notebook
Next-generation protein-protein interaction site (PPIS) prediction integrating ESM-2 protein language model representations with structural & evolutionary features via biophysics-supervised gated fusion and equivariant graph networks.
bioinformatics deep-learning pytorch protein-protein-interaction graph-neural-networks protein-structures graph-transformer egnn esm2 ppis-prediction
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Oct 8, 2026 - Python
Antimicrobial peptide discovery via ESM-2 fine-tuning. LoRA training on ESCAPE/GenPept-Curated-2025/PepBenchmark with multilabel evaluation.
machine-learning bioinformatics drug-discovery lora antimicrobial-peptides protein-language-model esm2
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Jun 2, 2026 - Python
Do protein foundation models help predict peptide-HLA class I complex stability on unseen binding grooves? No: a conventional supervised net beats all eleven PLM configurations tested. London AI x Science Hackathon 2026, Serova track.
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Oct 5, 2026 - Python
Similarity search for protein sequences using ESM-2 embeddings and Approximate Nearest Neighbor (ANN) methods.
bioinformatics blast twilight-zone protein-embeddings remote-homology-detection esm2 protein-similarity
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Feb 25, 2026 - Python
Experimental-design methods for budgeted protein-epistasis mapping with zero-shot ESM-2 signals; evaluated on GB1.
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Sep 1, 2026 - Python
Functional prediction and evidence-grounded interpretation of KCNH2 missense variants using MaveDB, ESM-2, XGBoost, ClinVar, AlphaMissense and RAG.
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Aug 1, 2026 - Jupyter Notebook
Zero-shot variant pathogenicity prediction via spectral covariance analysis of ESM2 hidden states | Claw4S 2026
bioinformatics computational-biology reproducibility clinvar spectral-analysis zero-shot variant-effect-prediction protein-language-model esm2 claw4s-2026
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Apr 22, 2026 - Python
Residue-residue contact prediction using ESM2 enhanced with template-based structural priors from homologous sequences.
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Oct 25, 2025 - Python
Dual-channel (quantitative + qualitative) predictor for cyclic peptide antimicrobial activity, with annotation learning for unseen cyclization chemistries
machine-learning cheminformatics drug-discovery lightgbm antimicrobial-peptides cyclic-peptides activity-prediction esm2 mic-prediction
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Nov 4, 2026 - Python
Transformer fusion pipeline for protein binding-site prediction using ESM2 protein embeddings, physicochemical surface descriptors, and neighbourhood-aware attention.
docker machine-learning bioinformatics deep-learning protein-structure transformers pytorch hydra drug-discovery structural-bioinformatics mlops pytorch-lightning protein-language-models esm2 binding-site-prediction
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Jun 29, 2026 - Python
Prédiction de la solubilité de protéines recombinantes depuis la séquence (ESM-2 150M fine-tuné + 13 descripteurs biochimiques), identification PDB/UniProt et plan d'expression/purification. Démo Gradio en ligne.
bioinformatics deep-learning pytorch gradio mlops github-actions huggingface protein-language-model protein-solubility esm2
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Nov 5, 2026 - Python
Bioinformatics Kaggle project for prime editing RT activity prediction using leave-one-family-out cross-validation and CLS-oriented modeling.
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Aug 14, 2026 - Jupyter Notebook
The protein-engineering design loop as one Rust binary: mutate, fold, QC folders of models into Parquet, ESM-2 variant scoring, a terminal viewer, and a GA4GH TES 1.1 server. Science validated against mdtraj, FreeSASA, cctbx and PLIP in CI.
rust machine-learning bioinformatics protein-structure computational-biology scientific-computing parquet ga4gh terminal-graphics biophysics protein-design dssp deep-mutational-scanning protein-engineering podman alphafold esmfold esm2 molprobity structure-validation
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Oct 21, 2026 - Rust
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
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