دورية أكاديمية
أعرض في EDS

Protein remote homology detection and structural alignment using deep learning.

التفاصيل البيبلوغرافية
العنوان: Protein remote homology detection and structural alignment using deep learning.
المؤلفون: Hamamsy T; Center for Data Science, New York University, New York, NY, USA., Morton JT; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA., Blackwell R; Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA., Berenberg D; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.; Prescient Design, New York, NY, USA., Carriero N; Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA., Gligorijevic V; Prescient Design, New York, NY, USA., Strauss CEM; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA., Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA., Cho K; Center for Data Science, New York University, New York, NY, USA. kc119@nyu.edu.; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA. kc119@nyu.edu.; Prescient Design, New York, NY, USA. kc119@nyu.edu.; CIFAR, Toronto, Ontario, Canada. kc119@nyu.edu., Bonneau R; Center for Data Science, New York University, New York, NY, USA. bonneaur@gene.com.; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA. bonneaur@gene.com.; Prescient Design, New York, NY, USA. bonneaur@gene.com.; Department of Biology, New York University, New York, NY, USA. bonneaur@gene.com.
المصدر: Nature biotechnology [Nat Biotechnol] 2024 Jun; Vol. 42 (6), pp. 975-985. Date of Electronic Publication: 2023 Sep 07.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE
أسماء مطبوعة: Publication: New York Ny : Nature America Publishing
Original Publication: New York, NY : Nature Pub. Co., [1996-
مواضيع طبية MeSH: Deep Learning* , Proteins*/chemistry , Sequence Alignment*/methods , Databases, Protein*, Sequence Analysis, Protein/methods ; Computational Biology/methods ; Algorithms ; Protein Conformation
مستخلص: Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure-structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.
(© 2023. The Author(s).)
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معلومات مُعتمدة: R35GM122515 National Science Foundation (NSF); IOS-1546218 National Science Foundation (NSF); R35 GM122515 United States GM NIGMS NIH HHS; R01 DK103358 United States DK NIDDK NIH HHS; CBET- 1728858 National Science Foundation (NSF); R01 AI130945 United States AI NIAID NIH HHS
المشرفين على المادة: 0 (Proteins)
تواريخ الأحداث: Date Created: 20230907 Date Completed: 20240616 Latest Revision: 20240620
رمز التحديث: 20240620
مُعرف محوري في PubMed: PMC11180608
DOI: 10.1038/s41587-023-01917-2
PMID: 37679542
قاعدة البيانات: MEDLINE
الوصف
تدمد:1546-1696
DOI:10.1038/s41587-023-01917-2