ProtNote: a multimodal method for protein-function annotation

S Char

doi:10.1093/bioinformatics/btaf170

2025-04-15

PRE

DOI：10.1093/bioinformatics/btaf170

原文链接

摘要

En 中文

动机理解蛋白质序列-功能关系对于推动蛋白质生物学和蛋白质工程的发展至关重要。然而，仅有<1%的已知蛋白质序列具有经过人工验证的功能。尽管深度学习方法已在蛋白质功能预测方面显示出潜力，但当前模型仅限于预测它们所训练的功能。结果在此，我们介绍了ProtNote，一种利用自由文本的多模态深度学习模型，以实现监督学习和零样本蛋白质功能预测。ProtNote不仅在其训练集的注释上保持了接近当前最佳的性能，还能在零样本测试设置中推广到未见过的和新型功能。通过捕捉精细的序列-功能关系，ProtNote在预测新型基因本体论注释和酶学委员会编号方面表现出优于基线模型的性能，从而解锁了先前模型无法访问的一系列生物学应用场景。我们设想，ProtNote将通过使科学家能够使用不受预定义标签限制的自由文本输入，来增强蛋白质功能发现——这是应对蛋白质生物学动态发展的必要能力。可用性与实现代码可在GitHub上获取：https://github.com/microsoft/protnote；模型权重、数据集和评估指标通过Zenodo提供：https://zenodo.org/records/13897920。

Keyword:

MODELS

期刊

Bioinformatics

IF:

5.4

论文数:

1.4K

被引数:

17.9W

机构

microsoft

学者数:

论文数: 8

被引数: 0

引用论文

Amino acid substitution matrices from protein blocks.来自蛋白质块的氨基酸取代矩阵。

Proceedings of the National Academy of Sciences

IF0

1992-11-15

OAAI

S Henikoff; J G Henikoff

The ENZYME database in 2000

NUCLEIC ACIDS RESEARCH

IF13.1

2000-01-01

1.0K

OAAI

Bairoch, A

Gene Ontology: tool for the unification of biology 基因本体论: 统一生物学的工具

NATURE GENETICS

IF31.8

2000-05-01

3.4W

OAAI

Ashburner, M; Ball, CA; Blake, JA; Botstein, D; Butler, H; Cherry, JM; Davis, AP; Dolinski, K; Dwight, SS; Eppig, JT; Harris, MA; Hill, DP; Issel-Tarver, L; Kasarskis, A; Lewis, S; Matese, JC; Richardson, JE; Ringwald, M; Rubin, GM; Sherlock, G

DeepGOPlus: improved protein function prediction from sequence Deepgeplus: 从序列中改进蛋白质功能预测

Bioinformatics

IF0

2021-05-03

OAAI

Maxat Kulmanov; Robert Hoehndorf

Fine-tuning protein language models boosts predictions across diverse tasks 微调蛋白质语言模型可提高跨不同任务的预测

NATURE COMMUNICATIONS

IF15.7

2024-08-28

OAAI

Schmirler, Robert; Heinzinger, Michael; Rost, Burkhard

ExPASy: the proteomics server for in-depth protein knowledge and analysis ExPASy: 用于深入蛋白质知识和分析的蛋白质组学服务器

NUCLEIC ACIDS RESEARCH

IF13.1

2003-07-01

4.8K

OAAI

Gasteiger, E; Gattiker, A; Hoogland, C; Ivanyi, I; Appel, RD; Bairoch, A

The Gene Ontology knowledgebase in 2023 基因本体知识库2023年

GENETICS

IF5.1

2023-03-03

774

OAAI

Aleksander, Suzi A.; Balhoff, James; Carbon, Seth; Cherry, J. Michael; Drabkin, Harold J.; Ebert, Dustin; Feuermann, Marc; Gaudet, Pascale; Harris, Nomi L.; Hill, David P.; Lee, Raymond; Mi, Huaiyu; Moxon, Sierra; Mungall, Christopher J.; Muruganugan, Anushya; Mushayahama, Tremayne; Sternberg, Paul W.; Thomas, Paul D.; Van Auken, Kimberly; Ramsey, Jolene; Siegele, Deborah A.; Chisholm, Rex L.; Fey, Petra; Aspromonte, Maria Cristina; Nugnes, Maria Victoria; Quaglia, Federica; Tosatto, Silvio; Giglio, Michelle; Nadendla, Suvarna; Antonazzo, Giulia; Attrill, Helen; dos Santos, Gil; Marygold, Steven; Strelets, Victor; Tabone, Christopher J.; Thurmond, Jim; Zhou, Pinglei; Ahmed, Saadullah H.; Asanitthong, Praoparn; Luna Buitrago, Diana; Erdol, Meltem N.; Gage, Matthew C.; Ali Kadhum, Mohamed; Li, Kan Yan Chloe; Long, Miao; Michalak, Aleksandra; Pesala, Angeline; Pritazahra, Armalya; Saverimuttu, Shirin C. C.; Su, Renzhi; Thurlow, Kate E.; Lovering, Ruth C.; Logie, Colin; Oliferenko, Snezhana; Blake, Judith; Christie, Karen; Corbani, Lori; Dolan, Mary E.; Sitnikov, Dmitry; Smith, Cynthia; Cuzick, Alayne; Seager, James; Cooper, Laurel; Elser, Justin; Jaiswal, Pankaj; Gupta, Parul; Naithani, Sushma; Lera-Ramirez, Manuel; Rutherford, Kim; Wood, Valerie; De Pons, Jeffrey L.; Dwinell, Melinda R.; Hayman, G. Thomas; Kaldunski, Mary L.; Kwitek, Anne E.; Laulederkind, Stanley J. F.; Tutaj, Marek A.; Vedi, Mahima; Wang, Shur-Jen; D'Eustachio, Peter; Aimo, Lucila; Axelsen, Kristian; Bridge, Alan; Hyka-Nouspikel, Nevila; Morgat, Anne; Engel, Stacia R.; Karra, Kalpana; Miyasato, Stuart R.; Nash, Robert S.; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Bakker, Erika; Berardini, Tanya Z.; Reiser, Leonore; Auchincloss, Andrea; Argoud-Puy, Ghislaine; Blatter, Marie-Claude; Boutet, Emmanuel; Breuza, Lionel; Casals-Casas, Cristina; Coudert, Elisabeth; Estreicher, Anne; Livia Famiglietti, Maria; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hulo, Chantal; Jungo, Florence; Le Mercier, Philippe; Lieberherr, Damien; Masson, Patrick; Pedruzzi, Ivo; Pourcel, Lucille; Poux, Sylvain; Rivoire, Catherine; Sundaram, Shyamala; Bateman, Alex; Bowler-Barnett, Emily; Bye-A-Jee, Hema; Denny, Paul; Ignatchenko, Alexandr; Ishtiaq, Rizwan; Lock, Antonia; Lussi, Yvonne; Magrane, Michele; Martin, Maria J.; Orchard, Sandra; Raposo, Pedro; Speretta, Elena; Tyagi, Nidhi; Warner, Kate; Zaru, Rossana; Diehl, Alexander D.; Chan, Juancarlos; Diamantakis, Stavros; Raciti, Daniela; Zarowiecki, Magdalena; Fisher, Malcolm; James-Zorn, Christina; Ponferrada, Virgilio; Zorn, Aaron; Ramachandran, Sridhar; Ruzicka, Leyla; Westerfield, Monte

Proteins in Synthetic Biology with Agricultural and Environmental Applications 合成生物学中具有农业和环境应用前景的蛋白质

SynBio

IF0

2022-11-21

OAAI

Madison M. Mann; Toriana N. Vigil; Samantha M. Felton; William E. Fahy; Mason A. Kinkeade; Victoria K. Kartseva; Mary-Jean C. Rowson; Abigail J. Frost; Bryan W. Berger

Multilingual E5 text embeddings: a technical report 多语言E5文本嵌入：一份技术报告

IF0

OAAI

Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing 面向生物医学自然语言处理的领域语言模型预训练

ACM Transactions on Computing for Healthcare

IF0

2021-10-15

OAAI

Yu Gu; Robert Tinn; Hao Cheng; Michael Lucas; Naoto Usuyama; Xiaodong Liu; Tristan Naumann; Jianfeng Gao; Hoifung Poon

查看更多内容