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protein design

32 papers

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Co-occurring keywords

generative model (2892) protein language model (40) protein structure (59) diffusion model (3751) protein structure prediction (26) protein sequence (27) bayesian optimization (624) biological sequence design (6) graph neural network (3962) inverse protein folding (4)

Papers

Advancing Protein Design via Multi-Agent Reinforcement Learning with Pareto-Based Collaborative Optimization AAAI 2026
DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design AAAI 2026
Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics AAAI 2026
Protein Large Language Models: A Comprehensive Survey EMNLP 2025
Controllable Protein Sequence Generation with LLM Preference Optimization AAAI 2025
UniIF: Unified Molecule Inverse Folding NIPS 2024
Bridge-IF: Learning Inverse Protein Folding with Markov Bridges NIPS 2024
Generating Highly Designable Proteins with Geometric Algebra Flow Matching NIPS 2024
Geometric Trajectory Diffusion Models NIPS 2024
Functional Graphical Models: Structure Enables Offline Data-Driven Optimization AISTATS 2024
Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning AAAI 2024
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses ACL 2024
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Generation NIPS 2024
Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient NIPS 2024
OpenProteinSet: Training data for structural biology at scale NIPS 2023
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds ICML 2023
Extrapolative Controlled Sequence Generation via Iterative Refinement ICML 2023
AbODE: Ab initio antibody design using conjoined ODEs ICML 2023
Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences NIPS 2023
Structure-informed Language Models Are Protein Designers ICML 2023
Protein Design with Guided Discrete Diffusion NIPS 2023
Practical and Asymptotically Exact Conditional Sampling in Diffusion Models NIPS 2023
Full-Atom Protein Pocket Design via Iterative Refinement NIPS 2023
ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers NIPS 2023
ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics NIPS 2023