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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
OpenProteinSet: Training data for structural biology at scaleCode4
Galactica: A Large Language Model for ScienceCode4
Robust deep learning based protein sequence design using ProteinMPNNCode3
Highly accurate protein structure prediction with AlphaFoldCode3
MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction ModelsCode2
Protein Large Language Models: A Comprehensive SurveyCode2
MotifBench: A standardized protein design benchmark for motif-scaffolding problemsCode2
PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOLCode2
Training on test proteins improves fitness, structure, and function predictionCode2
SE(3) diffusion model with application to protein backbone generationCode2
Protein structure generation via folding diffusionCode2
State-specific protein-ligand complex structure prediction with a multi-scale deep generative modelCode2
FastFold: Reducing AlphaFold Training Time from 11 Days to 67 HoursCode2
ProteinBERT: a universal deep-learning model of protein sequence and functionCode2
Distribution-Free, Risk-Controlling Prediction SetsCode2
Conformation-Aware Structure Prediction of Antigen-Recognizing Immune ProteinsCode1
Towards Interpretable Protein Structure Prediction with Sparse AutoencodersCode1
Deep Learning of Proteins with Local and Global Regions of DisorderCode1
Generative diffusion model with inverse renormalization group flowsCode1
FoldMark: Protecting Protein Generative Models with WatermarkingCode1
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence LearningCode1
MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-TrainingCode1
Accurate and efficient protein embedding using multi-teacher distillation learningCode1
A Hitchhiker's Guide to Geometric GNNs for 3D Atomic SystemsCode1
AtomSurf : Surface Representation for Learning on Protein StructuresCode1
Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoopCode1
Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment GenerationCode1
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain PackingCode1
CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learningCode1
EigenFold: Generative Protein Structure Prediction with Diffusion ModelsCode1
Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure PredictionCode1
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue CloudsCode1
ExplainableFold: Understanding AlphaFold Prediction with Explainable AICode1
RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA DesignCode1
Protein Language Models and Structure Prediction: Connection and ProgressionCode1
Geometry-Complete Perceptron Networks for 3D Molecular GraphsCode1
A Graph Neural Network Approach to Automated Model Building in Cryo-EM MapsCode1
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence UnderstandingCode1
Generative De Novo Protein Design with Global ContextCode1
Iterative SE(3)-TransformersCode1
SidechainNet: An All-Atom Protein Structure Dataset for Machine LearningCode1
Energy-based models for atomic-resolution protein conformationsCode1
PolyFold: an interactive visual simulator for distance-based protein foldingCode1
Accurate Protein Structure Prediction by Embeddings and Deep Learning RepresentationsCode1
ProteinNet: a standardized data set for machine learning of protein structureCode1
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
Transformers in Protein: A Survey—0
Unfolding AlphaFold's Bayesian Roots in Probability Kinematics—0
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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