A Text-guided Protein Design Framework

• URL: http://arxiv.org/abs/2302.04611v3
• Date: Mon, 12 Aug 2024 16:05:43 GMT
• Title: A Text-guided Protein Design Framework
• Authors: Shengchao Liu, Yanjing Li, Zhuoxinran Li, Anthony Gitter, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Arvind Ramanathan, Chaowei Xiao, Jian Tang, Hongyu Guo, Anima Anandkumar,
• Abstract summary: We propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP which aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that creates the protein sequences from the representation. We quantitatively verify the effectiveness of ProteinDT on three challenging tasks: (1) over 90% accuracy for text-guided protein generation; (2) best hit ratio on 12 zero-shot text-guided protein editing tasks; (3) superior performance on four out of six protein property prediction benchmarks.
• Score: 106.79061950107922
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level functionalities. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP which aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that creates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We quantitatively verify the effectiveness of ProteinDT on three challenging tasks: (1) over 90\% accuracy for text-guided protein generation; (2) best hit ratio on 12 zero-shot text-guided protein editing tasks; (3) superior performance on four out of six protein property prediction benchmarks.

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