An implementation of ESM2 in Equinox+JAX
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Apr 20, 2026 - Python
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esm2
Here are 85 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
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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Sep 25, 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
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
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
Residue-residue contact prediction using ESM2 enhanced with template-based structural priors from homologous sequences.
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Oct 25, 2025 - 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
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
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
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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Sep 24, 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
RCSF-AMP: residue-confidence-guided sequence-structure fusion for antimicrobial peptide prediction
bioinformatics deep-learning pytorch protein fusion cross-modal mamba graph-neural-network esm2 antimicrobial-peptide
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Aug 29, 2026 - Python
Protein language model framework for functional annotation of marine phage dark matter. Ibdaa 2027 — Computational Biology & Bioinformatics.
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Aug 12, 2026 - Python
Dual-scale peptide property prediction with atom/residue encoders and cross-attention fusion.
bioinformatics pytorch drug-discovery rdkit multimodal-learning peptide-prediction cross-attention protein-ai esm2 peptide-ai
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Apr 19, 2026 - Jupyter Notebook
Fine-tuning ESM-2 with LoRA for enzyme family classification. Homology-aware splitting, calibrated uncertainty, integrated gradients interpretability, and FastAPI inference. Built for production.
structural-biology pytorch drug-discovery lora uncertainty-quantification interpretability fine-tuning enzyme-classification protein-language-model esm2
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Jun 6, 2026 - Python
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