Cover Image

Quantifying the Role of OpenFold Components in Protein Structure Prediction

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Hayes, Tyler L., Krishnan, Giri P.
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Artificial Intelligence
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights
by: Fang, Xiaomin, et al.
Published: (2024)

ConforNets: Latents-Based Conformational Control in OpenFold3
by: Lee, Minji, et al.
Published: (2026)

Atom-level Protein Representation Learning Improves Protein Structure Prediction
by: Kim, Taewon, et al.
Published: (2026)

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

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

Technical Report of HelixFold3 for Biomolecular Structure Prediction
by: Liu, Lihang, et al.
Published: (2024)

Bridge-IF: Learning Inverse Protein Folding with Markov Bridges
by: Zhu, Yiheng, et al.
Published: (2024)

FoldToken: Learning Protein Language via Vector Quantization and Beyond
by: Gao, Zhangyang, et al.
Published: (2024)

Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
by: Parsan, Nithin, et al.
Published: (2025)

Non-Canonical Crosslinks Confound Evolutionary Protein Structure Models
by: Lacombe, Romain
Published: (2025)

BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction
by: Wang, Xin, et al.
Published: (2025)

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
by: Wei, Chen, et al.
Published: (2026)

Advanced Deep Learning Methods for Protein Structure Prediction and Design
by: Zhang, Yichao, et al.
Published: (2025)

Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation
by: Giri, Nabin, et al.
Published: (2026)

ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models
by: Ma, Zicheng, et al.
Published: (2025)

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
by: Wu, Lirong, et al.
Published: (2024)

Speak to a Protein: An Interactive Multimodal Co-Scientist for Protein Analysis
by: Navarro, Carles, et al.
Published: (2025)

Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning
by: Espitia, Giovanny, et al.
Published: (2024)

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
by: Chen, Bo, et al.
Published: (2024)

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

Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
by: Jiao, Xiaoran, et al.
Published: (2024)

A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design
by: Dai, Weihang
Published: (2025)

CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design
by: Gao, Zijun, et al.
Published: (2025)

Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures
by: Liu, Ce, et al.
Published: (2024)

Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
by: Ko, Eunji, et al.
Published: (2024)

Group Ligands Docking to Protein Pockets
by: Guan, Jiaqi, et al.
Published: (2025)

Controlling Repetition in Protein Language Models
by: Zhang, Jiahao, et al.
Published: (2026)

Are Protein Language Models Compute Optimal?
by: Serrano, Yaiza, et al.
Published: (2024)

Lattice Protein Folding with Variational Annealing
by: Khandoker, Shoummo Ahsan, et al.
Published: (2025)

One-step Structure Prediction and Screening for Protein-Ligand Complexes using Multi-Task Geometric Deep Learning
by: He, Kelei, et al.
Published: (2024)

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

The Dance of Atoms-De Novo Protein Design with Diffusion Model
by: Qin, Yujie, et al.
Published: (2025)

Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement
by: Singh, Lakshaditya, et al.
Published: (2025)

Constrained Diffusion for Protein Design with Hard Structural Constraints
by: Christopher, Jacob K., et al.
Published: (2025)

TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles
by: Xu, Yaoyao, et al.
Published: (2025)

AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
by: Jiang, Zixuan, et al.
Published: (2025)

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model
by: Lv, Changze, et al.
Published: (2025)

AMix-2: Establishing Protein as a Native Modality in Large Language Models
by: Qiu, Keyue, et al.
Published: (2026)

Multi-level Interaction Modeling for Protein Mutational Effect Prediction
by: Mo, Yuanle, et al.
Published: (2024)

Graph-level Protein Representation Learning by Structure Knowledge Refinement
by: Wang, Ge, et al.
Published: (2024)