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Protein Structure Prediction

Image credit: FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours

Papers

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Showing 1–50 of 188 papers

TitleStatusHype
Conformation-Aware Structure Prediction of Antigen-Recognizing Immune ProteinsCode1
MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction ModelsCode2
Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion—0
Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data—0
Aligning Protein Conformation Ensemble Generation with Physical Feedback—0
Unfolding AlphaFold's Bayesian Roots in Probability Kinematics—0
Transformers in Protein: A Survey—0
PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural modelsCode0
LightNobel: Improving Sequence Length Limitation in Protein Structure Prediction Model via Adaptive Activation Quantization—0
AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy—0
Cognitio Emergens: Agency, Dimensions, and Dynamics in Human-AI Knowledge Co-Creation—0
Exploring zero-shot structure-based protein fitness prediction—0
From sequence to protein structure and conformational dynamics with AI/ML—0
AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification—0
PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks—0
Advanced Deep Learning Methods for Protein Structure Prediction and Design—0
Towards Interpretable Protein Structure Prediction with Sparse AutoencodersCode1
Non-Canonical Crosslinks Confound Evolutionary Protein Structure Models—0
Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2—0
A Model-Centric Review of Deep Learning for Protein Design—0
Protein Large Language Models: A Comprehensive SurveyCode2
MotifBench: A standardized protein design benchmark for motif-scaffolding problemsCode2
Deep Learning of Proteins with Local and Global Regions of DisorderCode1
PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOLCode2
CENTS: Generating synthetic electricity consumption time series for rare and unseen scenarios—0
Human Genome Book: Words, Sentences and ParagraphsCode0
Computational Protein Science in the Era of Large Language Models (LLMs)—0
Generative diffusion model with inverse renormalization group flowsCode1
A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design—0
Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning—0
Applications of Knot Theory for the Improvement of the AlphaFold Protein Database—0
Training on test proteins improves fitness, structure, and function predictionCode2
Ratio law: mathematical descriptions for a universal relationship between AI performance and input samples—0
Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps—0
FoldMark: Protecting Protein Generative Models with WatermarkingCode1
CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin EvaluationCode0
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction—0
pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2Code0
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence LearningCode1
Recent advances in interpretable machine learning using structure-based protein representations—0
CrysAtom: Distributed Representation of Atoms for Crystal Property Prediction—0
Leveraging Deep Generative Model For Computational Protein Design And Optimization—0
Technical Report of HelixFold3 for Biomolecular Structure Prediction—0
MultiMed: Massively Multimodal and Multitask Medical Understanding—0
AlphaFolding: 4D Diffusion for Dynamic Protein Structure Prediction with Reference and Motion Guidance—0
Dihedral Angle Adherence: Evaluating Protein Structure Predictions in the Absence of Experimental Data—0
MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-TrainingCode1
Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation—0
cryoSPHERE: Single-particle heterogeneous reconstruction from cryo EM—0
Accurate and efficient protein embedding using multi-teacher distillation learningCode1
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All datasetsCASPSeqCASPSimSeqPaenSeqUniProtSeq

Benchmark Results

#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity20.62—Unverified
2GAL 1.3BValidation perplexity17.58—Unverified
3GAL 6.7BValidation perplexity17.29—Unverified
4GAL 30BValidation perplexity17.27—Unverified
5GAL 120BValidation perplexity17.26—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity19.18—Unverified
2GAL 1.3BValidation perplexity17.04—Unverified
3GAL 6.7BValidation perplexity16.35—Unverified
4GAL 30BValidation perplexity15.42—Unverified
5GAL 120BValidation perplexity12.77—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity16.35—Unverified
2GAL 1.3BValidation perplexity12.53—Unverified
3GAL 6.7BValidation perplexity7.76—Unverified
4GAL 30BValidation perplexity4.28—Unverified
5GAL 120BValidation perplexity3.14—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity19.05—Unverified
2GAL 1.3BValidation perplexity15.82—Unverified
3GAL 6.7BValidation perplexity11.58—Unverified
4GAL 30BValidation perplexity8.23—Unverified
5GAL 120BValidation perplexity5.54—Unverified