Cover Image

Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Xin, Ma, Si, Dong
Format:	Preprint
Published:	2024
Subjects:	Quantitative Methods Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Hallucinations in AlphaFold3 for Intrinsically Disordered Proteins with disorder in Biological Process Residues
by: Gopalan, Shreya, et al.
Published: (2025)

Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold
by: Chib, Garima, et al.
Published: (2025)

ScaleFold: Reducing AlphaFold Initial Training Time to 10 Hours
by: Zhu, Feiwen, et al.
Published: (2024)

actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions
by: Varga, Julia K., et al.
Published: (2024)

CryoLVM: Self-supervised Learning from Cryo-EM Density Maps with Large Vision Models
by: Fu, Weining, et al.
Published: (2026)

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
by: Tan, Cheng, et al.
Published: (2025)

PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
by: Mahbub, Sazan, et al.
Published: (2025)

Deep Learning Framework for RNA Inverse Folding with Geometric Structure Potentials
by: Yao, Annabelle
Published: (2025)

SimpleFold: Folding Proteins is Simpler than You Think
by: Wang, Yuyang, et al.
Published: (2025)

Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning
by: Wee, JunJie, et al.
Published: (2024)

Gaussian Mixture Model-Based Focused Refinement for Enhanced Flexible Structure Determination in CryoEM and CryoET
by: Chen, Muyuan
Published: (2026)

DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map
by: Luo, Deng, et al.
Published: (2024)

FoldSAE: Learning to Steer Protein Folding Through Sparse Representations
by: Zarzecki, Wojciech, et al.
Published: (2025)

Protein Fold Classification at Scale: Benchmarking and Pretraining
by: Chen, Dexiong, et al.
Published: (2026)

Learning the Language of Protein Structure
by: Gaujac, Benoit, et al.
Published: (2024)

Sparse Autoencoders for Low-$N$ Protein Function Prediction and Design
by: Tsui, Darin, et al.
Published: (2025)

DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images
by: Murad, Taslim, et al.
Published: (2024)

Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation
by: Wee, JunJie, et al.
Published: (2024)

Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
by: Cao, Hanqun, et al.
Published: (2025)

DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
by: Xie, Jiaqing, et al.
Published: (2024)

PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps
by: Bal, Rakesh, et al.
Published: (2023)

EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions
by: Nguyen, Ngoc-Quang
Published: (2025)

Improving AlphaFlow for Efficient Protein Ensembles Generation
by: Li, Shaoning, et al.
Published: (2024)

Optimizing Mirror-Image Peptide Sequence Design for Data Storage via Peptide Bond Cleavage Prediction
by: Lu, Yilong, et al.
Published: (2025)

GastroDL-Fusion: A Dual-Modal Deep Learning Framework Integrating Protein-Ligand Complexes and Gene Sequences for Gastrointestinal Disease Drug Discovery
by: Gao, Ziyang, et al.
Published: (2025)

PLA-SGCN: Protein-Ligand Binding Affinity Prediction by Integrating Similar Pairs and Semi-supervised Graph Convolutional Network
by: Abbasi, Karim, et al.
Published: (2024)

Deep Learning Model for Amyloidogenicity Prediction using a Pre-trained Protein LLM
by: Yagoub, Zohra, et al.
Published: (2025)

Low-N Protein Activity Optimization with FolDE
by: Roberts, Jacob B., et al.
Published: (2025)

Identification of Capture Phases in Nanopore Protein Sequencing Data Using a Deep Learning Model
by: Martin, Annabelle, et al.
Published: (2025)

ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals
by: Mitra, Shania, et al.
Published: (2024)

Prot2Token: A Unified Framework for Protein Modeling via Next-Token Prediction
by: Pourmirzaei, Mahdi, et al.
Published: (2025)

Molecular Odor Prediction with Harmonic Modulated Feature Mapping and Chemically-Informed Loss
by: Xie, HongXin, et al.
Published: (2025)

Better Protein Function Prediction by Modeling Survivorship Bias
by: Chao, Zhongmou, et al.
Published: (2026)

RNA-Protein Interaction Prediction Based on Deep Learning: A Comprehensive Survey
by: Li, Danyu, et al.
Published: (2024)

Protein-Mamba: Biological Mamba Models for Protein Function Prediction
by: Xu, Bohao, et al.
Published: (2024)

ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning
by: Wang, Ziwen, et al.
Published: (2025)

Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
by: Wu, Lirong, et al.
Published: (2024)

CodonMPNN for Organism Specific and Codon Optimal Inverse Folding
by: Stark, Hannes, et al.
Published: (2024)

Drug-Target Interaction/Affinity Prediction: Deep Learning Models and Advances Review
by: Vefghi, Ali, et al.
Published: (2025)

Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows
by: Rao, Yaochen, et al.
Published: (2026)