Cover Image

PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Zhang, Ruochi, Wu, Haoran, Liu, Chang, Li, Huaping, Wu, Yuqian, Li, Kewei, Wang, Yifan, Deng, Yifan, Chen, Jiahui, Zhou, Fengfeng, Gao, Xin
Format:	Preprint
Published:	2024
Subjects:	Machine Learning Artificial Intelligence Computational Engineering, Finance, and Science Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides
by: Li, Kewei, et al.
Published: (2024)

PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling
by: Chen, Tianlai, et al.
Published: (2023)

Remodeling Peptide-MHC-TCR Triad Binding as Sequence Fusion for Immunogenicity Prediction
by: Ma, Jiahao, et al.
Published: (2025)

Target-Specific De Novo Peptide Binder Design with DiffPepBuilder
by: Wang, Fanhao, et al.
Published: (2024)

NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
by: Guo, Tao, et al.
Published: (2025)

StaPep: an open-source tool for the structure prediction and feature extraction of hydrocarbon-stapled peptides
by: Wang, Zhe, et al.
Published: (2024)

PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation
by: Wang, Leyao, et al.
Published: (2024)

STELLA: A Multimodal LLM for Protein Functional Annotation via Unified Sequence-Structure Encoding
by: Xiao, Hongwang, et al.
Published: (2025)

MP2D: Constrained Monte Carlo Tree-Guided Diffusion for Multi-Objective Protein Sequence Design
by: Kong, Zitai, et al.
Published: (2026)

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

Dihedral Angle Adherence: Evaluating Protein Structure Predictions in the Absence of Experimental Data
by: Azeem, Musa, et al.
Published: (2024)

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
by: Tang, Sophia, et al.
Published: (2024)

ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing
by: Lv, Liuzhenghao, et al.
Published: (2024)

Physicochemically Informed Dual-Conditioned Generative Model of T-Cell Receptor Variable Regions for Cellular Therapy
by: Ma, Jiahao, et al.
Published: (2025)

CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization
by: Ge, Cheng, et al.
Published: (2025)

Constrained Shape Analysis with Applications to RNA Structure
by: Mardia, Kanti V., et al.
Published: (2025)

PepGB: Facilitating peptide drug discovery via graph neural networks
by: Lei, Yipin, et al.
Published: (2024)

SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
by: Ma, Runze, et al.
Published: (2024)

AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation
by: Liu, Lijun, et al.
Published: (2024)

Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models
by: Liu, Lihang, et al.
Published: (2023)

Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing
by: Ma, Zheng, et al.
Published: (2024)

Zero-Shot 3D Drug Design by Sketching and Generating
by: Long, Siyu, et al.
Published: (2022)

LSMTCR: A Scalable Multi-Architecture Model for Epitope-Specific T Cell Receptor de novo Design
by: Zhang, Ruihao, et al.
Published: (2025)

Molecular Dynamics Simulations Reveal PolyQ-Length-Dependent Conformational Changes in Huntingtin Exon-1: Implications for Environmental Co-Solvent Modulation of Aggregation-Prone States
by: Geddes-Nelson, Jai, et al.
Published: (2026)

A Hierarchical Adaptive Diffusion Model for Flexible Protein-Protein Docking
by: Yin, Rujie, et al.
Published: (2025)

CMADiff: Cross-Modal Aligned Diffusion for Controllable Protein Generation
by: Zhou, Changjian, et al.
Published: (2025)

Single-Sequence-Based Protein Secondary Structure Prediction using One-Hot and Chemical Encodings of Amino Acids
by: Trinh, Hoa, et al.
Published: (2024)

Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs
by: Hu, Xiuyuan, et al.
Published: (2024)

Peptide Structure Prediction Using Counter-Diabatic Quantum Approximate Optimization Algorithm (CD-QAOA)
by: Yun, Sung Won, et al.
Published: (2026)

Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding
by: Li, Jiarui, et al.
Published: (2025)

PepINVENT: Generative peptide design beyond the natural amino acids
by: Geylan, Gökçe, et al.
Published: (2024)

Computational Protein Science in the Era of Large Language Models (LLMs)
by: Fan, Wenqi, et al.
Published: (2025)

CAME-AB: Cross-Modality Attention with Mixture-of-Experts for Antibody Binding Site Prediction
by: Li, Hongzong, et al.
Published: (2025)

Peptide Sequencing Via Protein Language Models
by: Pham, Thuong Le Hoai, et al.
Published: (2024)

RNA-GPT: Multimodal Generative System for RNA Sequence Understanding
by: Xiao, Yijia, et al.
Published: (2024)

Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing
by: Zhang, Xiang, 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)

3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling
by: Pei, Qizhi, et al.
Published: (2024)

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
by: Pei, Qizhi, et al.
Published: (2024)

ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
by: Xiao, Yijia, et al.
Published: (2024)