List of papers about Proteins Design using Deep Learning
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Dec 20, 2025
#
protein-design
Here are 148 public repositories matching this topic...
Protein Graph Library
python bioinformatics deep-learning structural-biology protein-data-bank protein-structure computational-biology pytorch protein drug-discovery rna interactome protein-design interactomics geometric-deep-learning ppi-networks graph-neural-networks pytorch-geometric gene-regulatory-networks dgl
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Dec 8, 2025 - Jupyter Notebook
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
machine-learning ddi deeplearning representation-learning ppi rna-structure-prediction protein-design dti protein-folding protein-structure-prediction biocomputing self-supervised-learning graph-networks protein-docking molecule-design
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Aug 21, 2025 - Python
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
jupyter-notebook dna rosetta rna-structure-prediction protein-design protein-folding protein-structure-prediction google-colab pyrosetta protein-docking
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Aug 12, 2024 - Jupyter Notebook
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
deep-learning neural-networks convolutional-neural-networks jupyter-notebooks language-model protein-design rna-design protein-structure-prediction graph-neural-networks diffusion-models protein-docking small-molecules
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Sep 22, 2025 - Jupyter Notebook
Official repository for the ProteinGym benchmarks
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Jul 21, 2025 - HTML
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
bioinformatics chemistry structural-biology molecular-structures protein-structure artificial-intelligence dna protein proteomics docking peptides molecular-biology protein-design protein-protein-interaction swarm-intelligence structural-bioinformatics protein-dna-interactions bioinformatics-tool glowworm-swarm-optimization protein-docking
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Sep 16, 2025 - Python
The Rosetta Bio-macromolecule modeling package.
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Dec 19, 2025 - C++
Versatile computational pipeline for processing protein structure data for deep learning applications.
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Feb 14, 2024 - Python
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
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Apr 21, 2024 - Python
Fitness landscape exploration sandbox for biological sequenc 8000 e design.
benchmarking machine-learning deep-learning deep-reinforcement-learning computational-biology bayesian-optimization protein-design
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Feb 16, 2023 - Jupyter Notebook
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
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Dec 27, 2022 - Python
MaSIF-neosurf: surface-based protein design for ternary complexes.
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Dec 4, 2025 - Python
Open source biolab
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Dec 10, 2024 - JavaScript
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
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Nov 19, 2025 - Python
A Unified Evaluation Suite for Protein Design
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Dec 13, 2025 - Python
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
protein protein-sequences representation-learning protein-design protein-function-prediction protein-fitness-prediction
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Sep 30, 2024 - Jupyter Notebook
BindCraft modified to make PyRosetta use and installation optional: no license needed
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Nov 30, 2025 - Python
Codes for our paper "Full-Atom Peptide Design with Geometric Latent Diffusion" (NeurIPS 2024)
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Apr 16, 2025 - Python
RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.
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Jan 24, 2023 - Python
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