InstructPro: Natural Language Guided Ligand-Binding Protein Design

TL;DR

InstructPro is a generative model that designs ligand-binding proteins guided by natural language instructions, overcoming data limitations and achieving high accuracy and generalization in protein-ligand binding predictions.

Contribution

The paper introduces InstructPro, a novel natural language-guided protein design model trained on a large-scale dataset, outperforming baselines and demonstrating strong zero-shot capabilities.

Findings

Achieves high AlphaFold3 ipTM scores and binding affinities on seen ligands.

Maintains robust zero-shot performance with substantial scores.

Scaling model size improves design quality and generalization.

Abstract

The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data bottleneck, we leverage the abundant natural language descriptions characterizing protein-ligand interactions. Here, we introduce InstructPro, a family of generative models that design proteins following the guidance of natural language instructions and ligand formulas. InstructPro produces protein sequences consistent with specified function descriptions and ligand targets. To enable training and evaluation, we develop InstructProBench, a large-scale dataset of 9.6 million (function description, ligand, protein) triples. We train two model variants -- InstructPro-1B and InstructPro-3B -- that substantially outperform strong baselines. InstructPro-1B achieves an AlphaFold3 ipTM of 0.918 and a binding affinity of -8.764 on seen ligands, while maintaining robust performance in a zero-shot setting with scores of 0.869 and -6.713, respectively. These results are accompanied by novelty scores of 70.1% and 68.8%, underscoring the model's ability to generalize beyond the training set. Furthermore, the model yields a superior binding free energy of -20.9 kcal/mol and an average of 5.82 intermolecular hydrogen bonds, validating its proficiency in designing high-affinity ligand-binding proteins. Notably, scaling to InstructPro-3B further improves the zero-shot ipTM to 0.882, binding affinity to -6.797, and binding free energy to -25.8 kcal/mol, demonstrating clear performance gains associated with increased model capacity. These findings highlight the power of natural language-guided generative models to mitigate the data bottlenecks in traditional structure-based methods, significantly broadening the scope of de novo protein design.