SOTAVerified

Protein Design

Formally, given the design requirements of users, models are required to generate protein amino acid sequences that align with those requirements.

Papers

Recently AddedMost HypedMost ActiveNeeds VerificationMost Verified

Showing 51–100 of 175 papers

TitleStatusHype
Learning from Protein Structure with Geometric Vector PerceptronsCode1
Energy-based models for atomic-resolution protein conformationsCode1
Toward the Explainability of Protein Language Models for Sequence Design—0
Geometric deep learning assists protein engineering. Opportunities and Challenges—0
Natural Language Guided Ligand-Binding Protein Design—0
Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction—0
AlphaFold Database Debiasing for Robust Inverse Folding—0
ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning—0
Improving Protein Sequence Design through Designability Preference Optimization—0
CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language ModelsCode0
Breaking the Performance Ceiling in Complex Reinforcement Learning requires Inference Strategies—0
Protein Design with Dynamic Protein Vocabulary—0
PDFBench: A Benchmark for De novo Protein Design from Function—0
DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design—0
PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural modelsCode0
Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and EvaluationCode0
ProT-GFDM: A Generative Fractional Diffusion Model for Protein Generation—0
Sparks: Multi-Agent Artificial Intelligence Model Discovers Protein Design Principles—0
The Dance of Atoms-De Novo Protein Design with Diffusion Model—0
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings—0
Prot42: a Novel Family of Protein Language Models for Target-aware Protein Binder Generation—0
Multi-Objective Quality-Diversity in Unstructured and Unbounded SpacesCode0
Advanced Deep Learning Methods for Protein Structure Prediction and Design—0
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models—0
Applying computational protein design to therapeutic antibody discovery -- current state and perspectives—0
A Model-Centric Review of Deep Learning for Protein Design—0
Agentic End-to-End De Novo Protein Design for Tailored Dynamics Using a Language Diffusion Model—0
Persistent Sheaf Laplacian Analysis of Protein FlexibilityCode0
Steering Protein Family Design through Profile Bayesian Flow—0
Fast and Accurate Antibody Sequence Design via Structure Retrieval—0
Iterative Importance Fine-tuning of Diffusion Models—0
A Variational Perspective on Generative Protein Fitness Optimization—0
Computational Protein Science in the Era of Large Language Models (LLMs)—0
Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and ReviewCode0
From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering—0
A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design—0
Multi-Attribute Constraint Satisfaction via Language Model Rewriting—0
Open-Source Protein Language Models for Function Prediction and Protein Design—0
ProtDAT: A Unified Framework for Protein Sequence Design from Any Protein Text Description—0
Building Confidence in Deep Generative Protein DesignCode0
MADE: Graph Backdoor Defense with Masked Unlearning—0
Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design—0
Beyond Human-Like Processing: Large Language Models Perform Equivalently on Forward and Backward Scientific TextCode0
Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab—0
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design—0
EMOCPD: Efficient Attention-based Models for Computational Protein Design Using Amino Acid Microenvironment—0
Training Free Guided Flow Matching with Optimal Control—0
MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models—0
What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs—0
Computational design of target-specific linear peptide binders with TransformerBeta—0
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Benchmark Results

#ModelMetricClaimedVerifiedStatus
1GraphTransPerplexity6.63—Unverified
2StructGNNPerplexity6.4—Unverified
3AlphaDesignPerplexity6.3—Unverified
4GCAPerplexity6.05—Unverified
5GVPPerplexity5.36—Unverified
6ProteinMPNNPerplexity4.61—Unverified
7PiFoldPerplexity4.55—Unverified
8Knowledge-DesignPerplexity3.46—Unverified
#ModelMetricClaimedVerifiedStatus
1ESM-IFPerplexity6.44—Unverified
2GVP-largePerplexity6.17—Unverified