Cover Image

Exploring AlphaFold 3 for CD47 Antibody-Antigen Binding Affinity: An Unexpected Discovery of Reverse docking

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Xu, Yiyang, Shen, Ziyou, Lv, Yanqing, Tan, Shutong, Sun, Chun, Zhang, Juan
Format:	Preprint
Published:	2025
Subjects:	Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

AlphaFold two years on: validation and impact
by: Kovalevskiy, Oleg, et al.
Published: (2024)

AlphaFold Database Debiasing for Robust Inverse Folding
by: Tan, Cheng, et al.
Published: (2025)

Inverse problems with experiment-guided AlphaFold
by: Maddipatla, Advaith, et al.
Published: (2025)

Precision Design of Cyclic Peptides using AlphaFold
by: Au, Cheuk Sau
Published: (2025)

Applications of Knot Theory for the Improvement of the AlphaFold Protein Database
by: Jahagirdar, Pranshu
Published: (2024)

Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2
by: Xing, Enming, et al.
Published: (2025)

State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences
by: Xing, Enming, et al.
Published: (2025)

AlphaFold2 for protein structure prediction: Best practices and critical analyses
by: Radjasandirane, Ragousandirane, et al.
Published: (2024)

AlphaFold Meets Flow Matching for Generating Protein Ensembles
by: Jing, Bowen, et al.
Published: (2024)

Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction
by: Chakravarty, Devlina, et al.
Published: (2024)

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

From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology
by: Abbaszadeh, Alireza, et al.
Published: (2025)

AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
by: Yuan, Zhongju, et al.
Published: (2023)

Structure-Aware Antibody Design with Affinity-Optimized Inverse Folding
by: Zhao, Xinyan, et al.
Published: (2025)

AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking
by: Liu, Chunan, et al.
Published: (2025)

ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings
by: Hanke, Josef, et al.
Published: (2026)

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

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics
by: Park, Hyun, et al.
Published: (2023)

Precise Antigen-Antibody Structure Predictions Enhance Antibody Development with HelixFold-Multimer
by: Gao, Jie, 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)

TopoBind: Multi-Modal Prediction of Antibody-Antigen Binding Free Energy via Sequence Embeddings and Structural Topology
by: Yu, Ciyuan, et al.
Published: (2025)

TerraBind: Fast and Accurate Binding Affinity Prediction through Coarse Structural Representations
by: Rossi, Matteo, et al.
Published: (2026)

ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Prediction
by: You, Zhang-Yu, et al.
Published: (2025)

Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction
by: Zia, Mushal, et al.
Published: (2024)

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization
by: Zhou, Xiangxin, et al.
Published: (2024)

HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3
by: Gao, Jie, et al.
Published: (2025)

ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha
by: Liu, Meng, et al.
Published: (2025)

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction
by: Zhang, Yupu, et al.
Published: (2025)

AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design
by: Zhao, Xinyan, et al.
Published: (2025)

Fold-switching Proteins
by: Chakravarty, Devlina, et al.
Published: (2025)

Decoding How Proteins Fold
by: Vila, Jorge
Published: (2025)

CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction
by: Han, Rong, et al.
Published: (2024)

Hybrid Quantum Neural Networks for Efficient Protein-Ligand Binding Affinity Prediction
by: Jeong, Seon-Geun, et al.
Published: (2025)

SPIN: SE(3)-Invariant Physics Informed Network for Binding Affinity Prediction
by: Choi, Seungyeon, et al.
Published: (2024)

Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties
by: Temizer, Asu Büşra, et al.
Published: (2022)

Structure-Aware Contrastive Learning with Fine-Grained Binding Representations for Drug Discovery
by: Lan, Jing, et al.
Published: (2025)

SeedFold: Scaling Biomolecular Structure Prediction
by: Zhou, Yi, et al.
Published: (2025)

Evaluation of In vitro anti-inflammatory activity and Insilico pharmacokinetics and molecular docking study of Horsfieldia iryaghedhi
by: HKK, Rajapaksha, et al.
Published: (2024)

End-to-End Reverse Screening Identifies Protein Targets of Small Molecules Using HelixFold3
by: Xu, Shengjie, et al.
Published: (2026)

IntFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction
by: The IntFold Team, et al.
Published: (2025)