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awesome-AI-based-protein-design
A collection of research papers for AI-based protein design
https://github.com/opendilab/awesome-AI-based-protein-design
- AlphaFold 2
- Accurate structure prediction of biomolecular interactions with AlphaFold 3
- A backbone-centred energy function of neural networks for protein design
- De novo protein design by deep network hallucination
- Design of protein-binding proteins from the target structure alone
- Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations
- Discovering de novo peptide substrates for enzymes using machine learning
- ECNet is an evolutionary context-integrated deep learning framework for protein engineering
- Protein design and variant prediction using autoregressive generative models
- Protein sequence design with a learned potential
- Protein design and variant prediction using autoregressive generative models
- Regression Transformer enables concurrent sequence regression and generation for molecular language modelling
- Controllable protein design with language models
- Robust deep learning based protein sequence design using ProteinMPNN
- Scaffolding protein functional sites using deep learning
- Deep Reinforcement Learning for Modelling Protein Complexes
- BERTology Meets Biology: Interpreting Attention in Protein Language Models
- Conditional Antibody Design as 3D Equivariant Graph Translation
- Conditioning by adaptive sampling for robust design
- Deep generative models create new and diverse protein structures
- Deep sharpening of topological features for de novo protein design
- Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design
- Generative modeling for protein structures
- Generative Models for Graph-Based Protein Design
- Model-based reinforcement learning for biological sequence design
- Molecule Generation For Target Protein Binding with Structural Motifs
- Protein Representation Learning by Geometric Structure Pretraining
- Protein generation with evolutionary diffusion: sequence is all you need
- A high-level programming language for generative protein design
- Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models
- Function-guided protein design by deep manifold sampling
- Language models generalize beyond natural proteins
- Language models of protein sequences at the scale of evolution enable accurate structure prediction
- TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs
- Language models generalize beyond natural proteins
- Fast and Flexible Protein Design Using Deep Graph Neural Networks
- Protein design and variant prediction using autoregressive generative models
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