[{"data":1,"prerenderedAt":532},["ShallowReactive",2],{"content-query-OZJiijqmrJ":3},{"_path":4,"_dir":5,"_draft":6,"_partial":6,"_locale":7,"title":8,"description":9,"date":10,"cover":11,"type":12,"body":13,"_type":526,"_id":527,"_source":528,"_file":529,"_stem":530,"_extension":531},"/news/en/2661","en",false,"","MindSpore SPONGE Suite Accelerates NMR Dynamic Structure Analysis of Proteins by 10 Times","Recently, working with teams of professors Gao Yiqin, Tian Changlin, and Wang Shenlin, Huawei has developed the iterative FAAST method of NMR.","2023-06-21","https://obs-mindspore-file.obs.cn-north-4.myhuaweicloud.com/file/2023/07/31/25de3f273de7427293049a7586023410.png","news",{"type":14,"children":15,"toc":523},"root",[16,24,30,35,43,48,53,58,63,70,75,82,87,92,97,102,107,112,117,122,126,130,134,139,144,149,154,159,164,169,174,179,184,189,194,199,204,209,214,219,224,229,233,238,243,247,252,257,262,267,272,276,281,285,290,295,300,305,310,315,320,325,330,335,340,345,349,354,359,364,369,374,379,384,389,394,399,404,409,414,419,424,428,433,438,443,448,453,458,465,470,475,480,485,490,495,500,513,518],{"type":17,"tag":18,"props":19,"children":21},"element","h1",{"id":20},"mindspore-sponge-suite-accelerates-nmr-dynamic-structure-analysis-of-proteins-by-10-times",[22],{"type":23,"value":8},"text",{"type":17,"tag":25,"props":26,"children":27},"p",{},[28],{"type":23,"value":29},"Recently, working with teams of professors Gao Yiqin, Tian Changlin, and Wang Shenlin, Huawei has developed the iterative folding assisted peak assignment (FAAST) method of nuclear magnetic resonance (NMR) based on the Ascend AI base software and hardware platform and MindSpore AI framework. The biocomputing suite MindSpore SPONGE cuts the time for NMR data analysis from months to hours, improving the efficiency by more than 10 times.",{"type":17,"tag":25,"props":31,"children":32},{},[33],{"type":23,"value":34},"Proteins are the main bearers of life activities. Obtaining protein structures is an indispensable link in modern drug R&D processes. Since drugs generally combine with target proteins in a solution environment, the solution (dynamic) structure of proteins is key to drug R&D and life activity research.",{"type":17,"tag":25,"props":36,"children":37},{},[38],{"type":17,"tag":39,"props":40,"children":42},"img",{"alt":7,"src":41},"https://obs-mindspore-file.obs.cn-north-4.myhuaweicloud.com/file/2023/07/31/47540831cf694e898649c85d50b62217.png",[],{"type":17,"tag":25,"props":44,"children":45},{},[46],{"type":23,"value":47},"Rhodanese domain of protein YgaP",{"type":17,"tag":25,"props":49,"children":50},{},[51],{"type":23,"value":52},"Solution structure (left) by NMR and crystal structure (right) by X-ray",{"type":17,"tag":25,"props":54,"children":55},{},[56],{"type":23,"value":57},"Existing calculation methods for protein structures, such as MEGA-Fold and AlphaFold, are mainly used to predict a single conformation[1][2]. It is difficult to tackle the error when the model prediction is inconsistent with the experimental information. Challenges, including how to use AI models to assist structure analysis in experiments and how to apply signals to improve structure prediction precision, are still looming. NMR is the only method that parses, with atomic resolution, the solution conformation and dynamic structure of proteins, which are close to the real situation[3]. However, this method is slow. On average, experts need to invest months in analyzing a single band of protein, and the analysis and attribution of experimental data takes the majority of time.",{"type":17,"tag":25,"props":59,"children":60},{},[61],{"type":23,"value":62},"To improve the speed and accuracy of NMR data analysis, Huawei has cooperated with teams of professors Gao Yiqin (Changping Laboratory, Biomedical Pioneering Innovation Centre (BIOPIC) of Beijing University), Tian Changlin (University of Science and Technology of China, High Magnetic Field Laboratory of the Chinese Academy of Science), and Wang Shenlin (State Key Laboratory of Bioreactor Engineering of East China University of Science and Technology). Based on Ascend AI and MindSpore, FAAST[4] is developed to automatically parse NMR data (NOESY spectrum), shortening the required time from months to hours. Related code has been open-sourced in the MindSpore SPONGE code repository on Gitee[5].",{"type":17,"tag":25,"props":64,"children":65},{},[66],{"type":17,"tag":39,"props":67,"children":69},{"alt":7,"src":68},"https://obs-mindspore-file.obs.cn-north-4.myhuaweicloud.com/file/2023/07/31/87ca91255e1e499884c9639ee52937bf.png",[],{"type":17,"tag":25,"props":71,"children":72},{},[73],{"type":23,"value":74},"NMR data analysis process of existing methods",{"type":17,"tag":25,"props":76,"children":77},{},[78],{"type":17,"tag":39,"props":79,"children":81},{"alt":7,"src":80},"https://obs-mindspore-file.obs.cn-north-4.myhuaweicloud.com/file/2023/07/31/7a9b023b0ac44e859908e4c0cbcf6d3a.png",[],{"type":17,"tag":25,"props":83,"children":84},{},[85],{"type":23,"value":86},"FAAST NMR data analysis process",{"type":17,"tag":25,"props":88,"children":89},{},[90],{"type":23,"value":91},"FAAST",{"type":17,"tag":25,"props":93,"children":94},{},[95],{"type":23,"value":96},"Experiment Group 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FAAST method integrates AI into a restraints-assisted structure predictor (RASP), which can generate protein structures that meet the structural restraints measured by NMR experiments. Based on the RASP model, FAAST can implement interactive iteration of data analysis and structure prediction, automatically parse NMR data, and obtain dynamic protein structures and structure restraint information. NMR data analysis time is greatly shortened without compromising the analysis precision, which is at the same level as that of domain experts.",{"type":17,"tag":25,"props":454,"children":455},{},[456],{"type":23,"value":457},"Analysis precision comparison",{"type":17,"tag":25,"props":459,"children":460},{},[461],{"type":17,"tag":39,"props":462,"children":464},{"alt":7,"src":463},"https://obs-mindspore-file.obs.cn-north-4.myhuaweicloud.com/file/2023/07/31/918bd17f876d4dca947403ac9d135b2c.png",[],{"type":17,"tag":25,"props":466,"children":467},{},[468],{"type":23,"value":469},"Comparison of time consumption in each phase of NMR methods",{"type":17,"tag":25,"props":471,"children":472},{},[473],{"type":23,"value":474},"The FAAST method greatly reduces the threshold for analysis NMR experimental data. Experts are freed from the demanding task of analysis, and can focus on experimental design and biological analysis of the obtained structure, promoting innovations in life science research and drug R&D processes.",{"type":17,"tag":25,"props":476,"children":477},{},[478],{"type":23,"value":479},"Boya distinguished professor Tang Chun, a researcher from the Center for Life Sciences, believes that the work can introduce not only NMR experimental restraints into structural prediction. For example, chemical cross-linking coupled with mass spectrometry (CXMS)[6] and fluorescence resonance energy transfer (FRET)[7] can be used as distance restraints complementary to each other to optimize protein structures. Therefore, the method developed by Gao Yiqin's team can also be widely used in integrative structural biology.",{"type":17,"tag":25,"props":481,"children":482},{},[483],{"type":23,"value":484},"[1] Jumper J, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2. Epub 2021 Jul 15. PMID: 34265844; PMCID: PMC8371605.",{"type":17,"tag":25,"props":486,"children":487},{},[488],{"type":23,"value":489},"[2] Liu S, Zhang J, Chu H, et al. PSP: million-level protein sequence dataset for protein structure prediction[J]. arXiv preprint arXiv:2206.12240, 2022.",{"type":17,"tag":25,"props":491,"children":492},{},[493],{"type":23,"value":494},"[3] Lutomski CA, El-Baba TJ, Robinson CV, Riek R, Scheres SHW, Yan N, AlQuraishi M, Gan L. The next decade of protein structure. Cell. 2022 Jul 21;185(15):2617-2620. doi: 10.1016/j.cell.2022.06.011. PMID: 35868264.",{"type":17,"tag":25,"props":496,"children":497},{},[498],{"type":23,"value":499},"[4] Liu S, Chu H, Xie Y, et al. Assisting and Accelerating NMR Assignment with Restrainted Structure Prediction[J]. bioRxiv, 2023: 2023.04. 14.536890.",{"type":17,"tag":25,"props":501,"children":502},{},[503,505],{"type":23,"value":504},"[5] ",{"type":17,"tag":506,"props":507,"children":511},"a",{"href":508,"rel":509},"https://gitee.com/mindspore/mindscience/tree/master/MindSPONGE/applications/research/FAAST",[510],"nofollow",[512],{"type":23,"value":508},{"type":17,"tag":25,"props":514,"children":515},{},[516],{"type":23,"value":517},"[6] Stahl, K., et al., Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Nat Biotechnol, 2023.",{"type":17,"tag":25,"props":519,"children":520},{},[521],{"type":23,"value":522},"[7] Tang, C. and Z. Gong, Integrating Non-NMR Distance Restraints to Augment NMR Depiction of Protein Structure and Dynamics. 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