Drug Target Binding

This repository organizes all assets for a Drug Target Binding study, including preprocessing scripts, analysis notebooks, datasets, and relevant literature.

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Literature

A curated list of important papers guiding this research.

Surveys

• A Survey on deep learning for drug-target binding prediction: models, benchmarks, evaluation, and case studies

  • Publication: Briefings in Bioinformatics, 2025, 26(5), bbaf491

• Large Language Models in Protein: A Comprehensive Survey

  • Publication: Findings of the Association for Computational Linguistics: EMNLP 2025

Research Papers

Paper	Code
Contrasting drugs from decoys	Code
Top-DTI: integrating topological deep learning and large language models for drug–target interaction prediction	Code
When Protein Structure Embedding Meets Large Language Models	Code

Other Relevant Repositories

A collection of external repositories that provide useful codebases, models, and paper lists related to protein docking.

• Protein-LLM-Survey: A comprehensive survey of Large Language Models in protein research, which includes a curated list of papers and code.